Merge pull request #147 from pegerto/m1_modfile

compile M1/M2 chip molfile plugin
small readme commit
2026-06-04 11:54:21 +08:00 · 2024-07-23 10:24:59 +02:00 · 2024-06-13 10:00:23 +01:00 · 2024-06-13 09:53:20 +01:00 · 2024-04-08 12:08:48 +02:00 · 2024-04-08 09:53:46 +00:00
1006 changed files with 87455 additions and 76203 deletions
--- a/22
+++ b/22
@@ -0,0 +1,22 @@
+FROM debian:bookworm-slim
+RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
+RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+
+RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]
--- a/README.md
+++ b/README.md
@@ -81,10 +81,10 @@ docker build -t fpocket/fpocket .
 This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using: 

 ```bash
-docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
+docker run -v `pwd`:/workdir fpocket/fpocket fpocket -f /workdir/yourfile.pdb
 ```

-Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
+Here you mount your current directory with your input files into the preconfigured `/workdir` in the docker container and then run fpocket on a file in that mounted folder. Make sure that the folder is writeable to others if you run it through docker.

 ### Installing

@@ -107,6 +107,11 @@ make ARCH=MACOSXX86_64
 sudo make install
 ```

+For M1 and M2, use the MACOSXARM64 architecture:
+```
+ARCH=MACOSXARM64 make
+```
+
 #### Using conda

 There's also a conda package of fpocket available thanks to Simon Bray. You can install fpocket using conda with:
--- a/data/sample/6a5k.cif
+++ b/data/sample/6a5k.cif
--- a/headers/atom.h
+++ b/headers/atom.h
@@ -37,12 +37,14 @@ typedef struct s_atm
    char name[5],		/**< Atom name */
         type[7],		/**< Atom type */
         chain[16],		/**< Chain name */
+         label_asym_id[16],
         symbol[3],		/**< Chemical symbol of the atom */
         res_name[8];		/**< Atom residue name */

    int id,			/**< Atom id */
        seen,                   /**< Say if we have seen this atom during a neighbor search */
        res_id,			/**< Atom residue ID */
+        label_seq_id,   /**<MMCIF label seq ID*/
        atype,
        charge,                 /**< Atom charge */
        abpa;                   /**< 1 if atom is an abpa, 0 otherwise*/	
--- a/headers/utils.h
+++ b/headers/utils.h
@@ -33,7 +33,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI

 /* ------------------------------- PUBLIC MACROS ---------------------------- */

-#define M_MAX_PDB_NAME_LEN 200  /**< maximum pdb filename length*/
+#define M_MAX_PDB_NAME_LEN 2000  /**< maximum pdb filename length*/
 #define M_MAX_CUSTOM_POCKET_LEN 8000 /** maximum length for a custom pocket string*/
 #define M_SIGN 1
 #define M_NO_SIGN 0
--- a/headers/writepdb.h
+++ b/headers/writepdb.h
@@ -28,6 +28,6 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom

 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[], 
 						 char alt_loc, const char res_name[], const char chain[], 
-						 int res_id, const char insert, float x, float y, float z, float occ, 
+						 int res_id,  const char label_asym_id[],int label_seq_id, const char insert, float x, float y, float z, float occ, 
 						 float bfactor, int abpa, const char *symbol, int charge,float abpa_prob) ;
 #endif
--- a/2
+++ b/2
@@ -1,7 +1,7 @@
 #------------------------------------------------------------
 # Makefile.
 #------------------------------------------------------------
-#ARCH	    = MACOSXX86_64
+# ARCH	    = MACOSXX86_64
 ARCH	    = LINUXAMD64
 export ARCH

--- a/plugins/MACOSXARM64/molfile/abinitplugin.so
+++ b/plugins/MACOSXARM64/molfile/abinitplugin.so
--- a/plugins/MACOSXARM64/molfile/amiraplugin.so
+++ b/plugins/MACOSXARM64/molfile/amiraplugin.so
--- a/plugins/MACOSXARM64/molfile/avsplugin.so
+++ b/plugins/MACOSXARM64/molfile/avsplugin.so
--- a/plugins/MACOSXARM64/molfile/babelplugin.so
+++ b/plugins/MACOSXARM64/molfile/babelplugin.so
--- a/plugins/MACOSXARM64/molfile/basissetplugin.so
+++ b/plugins/MACOSXARM64/molfile/basissetplugin.so
--- a/plugins/MACOSXARM64/molfile/bgfplugin.so
+++ b/plugins/MACOSXARM64/molfile/bgfplugin.so
--- a/plugins/MACOSXARM64/molfile/binposplugin.so
+++ b/plugins/MACOSXARM64/molfile/binposplugin.so
--- a/plugins/MACOSXARM64/molfile/biomoccaplugin.so
+++ b/plugins/MACOSXARM64/molfile/biomoccaplugin.so
--- a/plugins/MACOSXARM64/molfile/brixplugin.so
+++ b/plugins/MACOSXARM64/molfile/brixplugin.so
--- a/plugins/MACOSXARM64/molfile/carplugin.so
+++ b/plugins/MACOSXARM64/molfile/carplugin.so
--- a/plugins/MACOSXARM64/molfile/ccp4plugin.so
+++ b/plugins/MACOSXARM64/molfile/ccp4plugin.so
--- a/plugins/MACOSXARM64/molfile/corplugin.so
+++ b/plugins/MACOSXARM64/molfile/corplugin.so
--- a/plugins/MACOSXARM64/molfile/cpmdplugin.so
+++ b/plugins/MACOSXARM64/molfile/cpmdplugin.so
--- a/plugins/MACOSXARM64/molfile/crdplugin.so
+++ b/plugins/MACOSXARM64/molfile/crdplugin.so
--- a/plugins/MACOSXARM64/molfile/cubeplugin.so
+++ b/plugins/MACOSXARM64/molfile/cubeplugin.so
--- a/plugins/MACOSXARM64/molfile/dcdplugin.so
+++ b/plugins/MACOSXARM64/molfile/dcdplugin.so
--- a/plugins/MACOSXARM64/molfile/dlpolyplugin.so
+++ b/plugins/MACOSXARM64/molfile/dlpolyplugin.so
--- a/plugins/MACOSXARM64/molfile/dsn6plugin.so
+++ b/plugins/MACOSXARM64/molfile/dsn6plugin.so
--- a/plugins/MACOSXARM64/molfile/dtrplugin.so
+++ b/plugins/MACOSXARM64/molfile/dtrplugin.so
--- a/plugins/MACOSXARM64/molfile/dxplugin.so
+++ b/plugins/MACOSXARM64/molfile/dxplugin.so
--- a/plugins/MACOSXARM64/molfile/edmplugin.so
+++ b/plugins/MACOSXARM64/molfile/edmplugin.so
--- a/plugins/MACOSXARM64/molfile/fs4plugin.so
+++ b/plugins/MACOSXARM64/molfile/fs4plugin.so
--- a/plugins/MACOSXARM64/molfile/gamessplugin.so
+++ b/plugins/MACOSXARM64/molfile/gamessplugin.so
--- a/plugins/MACOSXARM64/molfile/graspplugin.so
+++ b/plugins/MACOSXARM64/molfile/graspplugin.so
--- a/plugins/MACOSXARM64/molfile/grdplugin.so
+++ b/plugins/MACOSXARM64/molfile/grdplugin.so
--- a/plugins/MACOSXARM64/molfile/gridplugin.so
+++ b/plugins/MACOSXARM64/molfile/gridplugin.so
--- a/plugins/MACOSXARM64/molfile/gromacsplugin.so
+++ b/plugins/MACOSXARM64/molfile/gromacsplugin.so
--- a/plugins/MACOSXARM64/molfile/jsplugin.so
+++ b/plugins/MACOSXARM64/molfile/jsplugin.so
--- a/plugins/MACOSXARM64/molfile/lammpsplugin.so
+++ b/plugins/MACOSXARM64/molfile/lammpsplugin.so
--- a/plugins/MACOSXARM64/molfile/libmolfile_plugin.a
+++ b/plugins/MACOSXARM64/molfile/libmolfile_plugin.a
--- a/plugins/MACOSXARM64/molfile/libmolfile_plugin.h
+++ b/plugins/MACOSXARM64/molfile/libmolfile_plugin.h
@@ -0,0 +1,415 @@
+#ifndef LIBMOLFILE_PLUGIN_H
+#define LIBMOLFILE_PLUGIN_H
+#include "vmdplugin.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int molfile_abinitplugin_init(void);
+extern int molfile_abinitplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_abinitplugin_fini(void);
+extern int molfile_amiraplugin_init(void);
+extern int molfile_amiraplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_amiraplugin_fini(void);
+extern int molfile_avsplugin_init(void);
+extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_avsplugin_fini(void);
+extern int molfile_babelplugin_init(void);
+extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_babelplugin_fini(void);
+extern int molfile_basissetplugin_init(void);
+extern int molfile_basissetplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_basissetplugin_fini(void);
+extern int molfile_bgfplugin_init(void);
+extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_bgfplugin_fini(void);
+extern int molfile_binposplugin_init(void);
+extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_binposplugin_fini(void);
+extern int molfile_biomoccaplugin_init(void);
+extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_biomoccaplugin_fini(void);
+extern int molfile_brixplugin_init(void);
+extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_brixplugin_fini(void);
+extern int molfile_carplugin_init(void);
+extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_carplugin_fini(void);
+extern int molfile_ccp4plugin_init(void);
+extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_ccp4plugin_fini(void);
+extern int molfile_corplugin_init(void);
+extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_corplugin_fini(void);
+extern int molfile_cpmdplugin_init(void);
+extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cpmdplugin_fini(void);
+extern int molfile_crdplugin_init(void);
+extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_crdplugin_fini(void);
+extern int molfile_cubeplugin_init(void);
+extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cubeplugin_fini(void);
+extern int molfile_dcdplugin_init(void);
+extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dcdplugin_fini(void);
+extern int molfile_dlpolyplugin_init(void);
+extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dlpolyplugin_fini(void);
+extern int molfile_dsn6plugin_init(void);
+extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dsn6plugin_fini(void);
+extern int molfile_dxplugin_init(void);
+extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dxplugin_fini(void);
+extern int molfile_edmplugin_init(void);
+extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_edmplugin_fini(void);
+extern int molfile_fs4plugin_init(void);
+extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_fs4plugin_fini(void);
+extern int molfile_gamessplugin_init(void);
+extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gamessplugin_fini(void);
+extern int molfile_graspplugin_init(void);
+extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_graspplugin_fini(void);
+extern int molfile_grdplugin_init(void);
+extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_grdplugin_fini(void);
+extern int molfile_gridplugin_init(void);
+extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gridplugin_fini(void);
+extern int molfile_gromacsplugin_init(void);
+extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gromacsplugin_fini(void);
+extern int molfile_jsplugin_init(void);
+extern int molfile_jsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_jsplugin_fini(void);
+extern int molfile_lammpsplugin_init(void);
+extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_lammpsplugin_fini(void);
+extern int molfile_mapplugin_init(void);
+extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mapplugin_fini(void);
+extern int molfile_mdfplugin_init(void);
+extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mdfplugin_fini(void);
+extern int molfile_mol2plugin_init(void);
+extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mol2plugin_fini(void);
+extern int molfile_moldenplugin_init(void);
+extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_moldenplugin_fini(void);
+extern int molfile_molemeshplugin_init(void);
+extern int molfile_molemeshplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_molemeshplugin_fini(void);
+extern int molfile_msmsplugin_init(void);
+extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_msmsplugin_fini(void);
+extern int molfile_namdbinplugin_init(void);
+extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_namdbinplugin_fini(void);
+extern int molfile_offplugin_init(void);
+extern int molfile_offplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_offplugin_fini(void);
+extern int molfile_parm7plugin_init(void);
+extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parm7plugin_fini(void);
+extern int molfile_parmplugin_init(void);
+extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parmplugin_fini(void);
+extern int molfile_pbeqplugin_init(void);
+extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pbeqplugin_fini(void);
+extern int molfile_pdbplugin_init(void);
+extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbplugin_fini(void);
+extern int molfile_pdbxplugin_init(void);
+extern int molfile_pdbxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbxplugin_fini(void);
+extern int molfile_phiplugin_init(void);
+extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_phiplugin_fini(void);
+extern int molfile_pltplugin_init(void);
+extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pltplugin_fini(void);
+extern int molfile_plyplugin_init(void);
+extern int molfile_plyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_plyplugin_fini(void);
+extern int molfile_pqrplugin_init(void);
+extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pqrplugin_fini(void);
+extern int molfile_psfplugin_init(void);
+extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_psfplugin_fini(void);
+extern int molfile_raster3dplugin_init(void);
+extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_raster3dplugin_fini(void);
+extern int molfile_rst7plugin_init(void);
+extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_rst7plugin_fini(void);
+extern int molfile_situsplugin_init(void);
+extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_situsplugin_fini(void);
+extern int molfile_spiderplugin_init(void);
+extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_spiderplugin_fini(void);
+extern int molfile_stlplugin_init(void);
+extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_stlplugin_fini(void);
+extern int molfile_tinkerplugin_init(void);
+extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_tinkerplugin_fini(void);
+extern int molfile_uhbdplugin_init(void);
+extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_uhbdplugin_fini(void);
+extern int molfile_vaspchgcarplugin_init(void);
+extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspchgcarplugin_fini(void);
+extern int molfile_vaspoutcarplugin_init(void);
+extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspoutcarplugin_fini(void);
+extern int molfile_vaspparchgplugin_init(void);
+extern int molfile_vaspparchgplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspparchgplugin_fini(void);
+extern int molfile_vaspposcarplugin_init(void);
+extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspposcarplugin_fini(void);
+extern int molfile_vasp5xdatcarplugin_init(void);
+extern int molfile_vasp5xdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vasp5xdatcarplugin_fini(void);
+extern int molfile_vaspxdatcarplugin_init(void);
+extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxdatcarplugin_fini(void);
+extern int molfile_vaspxmlplugin_init(void);
+extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxmlplugin_fini(void);
+extern int molfile_vtkplugin_init(void);
+extern int molfile_vtkplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vtkplugin_fini(void);
+extern int molfile_xbgfplugin_init(void);
+extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xbgfplugin_fini(void);
+extern int molfile_xsfplugin_init(void);
+extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xsfplugin_fini(void);
+extern int molfile_xyzplugin_init(void);
+extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xyzplugin_fini(void);
+extern int molfile_dtrplugin_init(void);
+extern int molfile_dtrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dtrplugin_fini(void);
+extern int molfile_maeffplugin_init(void);
+extern int molfile_maeffplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_maeffplugin_fini(void);
+
+#define MOLFILE_INIT_ALL \
+    molfile_abinitplugin_init(); \
+    molfile_amiraplugin_init(); \
+    molfile_avsplugin_init(); \
+    molfile_babelplugin_init(); \
+    molfile_basissetplugin_init(); \
+    molfile_bgfplugin_init(); \
+    molfile_binposplugin_init(); \
+    molfile_biomoccaplugin_init(); \
+    molfile_brixplugin_init(); \
+    molfile_carplugin_init(); \
+    molfile_ccp4plugin_init(); \
+    molfile_corplugin_init(); \
+    molfile_cpmdplugin_init(); \
+    molfile_crdplugin_init(); \
+    molfile_cubeplugin_init(); \
+    molfile_dcdplugin_init(); \
+    molfile_dlpolyplugin_init(); \
+    molfile_dsn6plugin_init(); \
+    molfile_dxplugin_init(); \
+    molfile_edmplugin_init(); \
+    molfile_fs4plugin_init(); \
+    molfile_gamessplugin_init(); \
+    molfile_graspplugin_init(); \
+    molfile_grdplugin_init(); \
+    molfile_gridplugin_init(); \
+    molfile_gromacsplugin_init(); \
+    molfile_jsplugin_init(); \
+    molfile_lammpsplugin_init(); \
+    molfile_mapplugin_init(); \
+    molfile_mdfplugin_init(); \
+    molfile_mol2plugin_init(); \
+    molfile_moldenplugin_init(); \
+    molfile_molemeshplugin_init(); \
+    molfile_msmsplugin_init(); \
+    molfile_namdbinplugin_init(); \
+    molfile_offplugin_init(); \
+    molfile_parm7plugin_init(); \
+    molfile_parmplugin_init(); \
+    molfile_pbeqplugin_init(); \
+    molfile_pdbplugin_init(); \
+    molfile_pdbxplugin_init(); \
+    molfile_phiplugin_init(); \
+    molfile_pltplugin_init(); \
+    molfile_plyplugin_init(); \
+    molfile_pqrplugin_init(); \
+    molfile_psfplugin_init(); \
+    molfile_raster3dplugin_init(); \
+    molfile_rst7plugin_init(); \
+    molfile_situsplugin_init(); \
+    molfile_spiderplugin_init(); \
+    molfile_stlplugin_init(); \
+    molfile_tinkerplugin_init(); \
+    molfile_uhbdplugin_init(); \
+    molfile_vaspchgcarplugin_init(); \
+    molfile_vaspoutcarplugin_init(); \
+    molfile_vaspparchgplugin_init(); \
+    molfile_vaspposcarplugin_init(); \
+    molfile_vasp5xdatcarplugin_init(); \
+    molfile_vaspxdatcarplugin_init(); \
+    molfile_vaspxmlplugin_init(); \
+    molfile_vtkplugin_init(); \
+    molfile_xbgfplugin_init(); \
+    molfile_xsfplugin_init(); \
+    molfile_xyzplugin_init(); \
+    molfile_dtrplugin_init(); \
+    molfile_maeffplugin_init(); \
+
+#define MOLFILE_REGISTER_ALL(v, cb) \
+    molfile_abinitplugin_register(v, cb); \
+    molfile_amiraplugin_register(v, cb); \
+    molfile_avsplugin_register(v, cb); \
+    molfile_babelplugin_register(v, cb); \
+    molfile_basissetplugin_register(v, cb); \
+    molfile_bgfplugin_register(v, cb); \
+    molfile_binposplugin_register(v, cb); \
+    molfile_biomoccaplugin_register(v, cb); \
+    molfile_brixplugin_register(v, cb); \
+    molfile_carplugin_register(v, cb); \
+    molfile_ccp4plugin_register(v, cb); \
+    molfile_corplugin_register(v, cb); \
+    molfile_cpmdplugin_register(v, cb); \
+    molfile_crdplugin_register(v, cb); \
+    molfile_cubeplugin_register(v, cb); \
+    molfile_dcdplugin_register(v, cb); \
+    molfile_dlpolyplugin_register(v, cb); \
+    molfile_dsn6plugin_register(v, cb); \
+    molfile_dxplugin_register(v, cb); \
+    molfile_edmplugin_register(v, cb); \
+    molfile_fs4plugin_register(v, cb); \
+    molfile_gamessplugin_register(v, cb); \
+    molfile_graspplugin_register(v, cb); \
+    molfile_grdplugin_register(v, cb); \
+    molfile_gridplugin_register(v, cb); \
+    molfile_gromacsplugin_register(v, cb); \
+    molfile_jsplugin_register(v, cb); \
+    molfile_lammpsplugin_register(v, cb); \
+    molfile_mapplugin_register(v, cb); \
+    molfile_mdfplugin_register(v, cb); \
+    molfile_mol2plugin_register(v, cb); \
+    molfile_moldenplugin_register(v, cb); \
+    molfile_molemeshplugin_register(v, cb); \
+    molfile_msmsplugin_register(v, cb); \
+    molfile_namdbinplugin_register(v, cb); \
+    molfile_offplugin_register(v, cb); \
+    molfile_parm7plugin_register(v, cb); \
+    molfile_parmplugin_register(v, cb); \
+    molfile_pbeqplugin_register(v, cb); \
+    molfile_pdbplugin_register(v, cb); \
+    molfile_pdbxplugin_register(v, cb); \
+    molfile_phiplugin_register(v, cb); \
+    molfile_pltplugin_register(v, cb); \
+    molfile_plyplugin_register(v, cb); \
+    molfile_pqrplugin_register(v, cb); \
+    molfile_psfplugin_register(v, cb); \
+    molfile_raster3dplugin_register(v, cb); \
+    molfile_rst7plugin_register(v, cb); \
+    molfile_situsplugin_register(v, cb); \
+    molfile_spiderplugin_register(v, cb); \
+    molfile_stlplugin_register(v, cb); \
+    molfile_tinkerplugin_register(v, cb); \
+    molfile_uhbdplugin_register(v, cb); \
+    molfile_vaspchgcarplugin_register(v, cb); \
+    molfile_vaspoutcarplugin_register(v, cb); \
+    molfile_vaspparchgplugin_register(v, cb); \
+    molfile_vaspposcarplugin_register(v, cb); \
+    molfile_vasp5xdatcarplugin_register(v, cb); \
+    molfile_vaspxdatcarplugin_register(v, cb); \
+    molfile_vaspxmlplugin_register(v, cb); \
+    molfile_vtkplugin_register(v, cb); \
+    molfile_xbgfplugin_register(v, cb); \
+    molfile_xsfplugin_register(v, cb); \
+    molfile_xyzplugin_register(v, cb); \
+    molfile_dtrplugin_register(v, cb); \
+    molfile_maeffplugin_register(v, cb); \
+
+#define MOLFILE_FINI_ALL \
+    molfile_abinitplugin_fini(); \
+    molfile_amiraplugin_fini(); \
+    molfile_avsplugin_fini(); \
+    molfile_babelplugin_fini(); \
+    molfile_basissetplugin_fini(); \
+    molfile_bgfplugin_fini(); \
+    molfile_binposplugin_fini(); \
+    molfile_biomoccaplugin_fini(); \
+    molfile_brixplugin_fini(); \
+    molfile_carplugin_fini(); \
+    molfile_ccp4plugin_fini(); \
+    molfile_corplugin_fini(); \
+    molfile_cpmdplugin_fini(); \
+    molfile_crdplugin_fini(); \
+    molfile_cubeplugin_fini(); \
+    molfile_dcdplugin_fini(); \
+    molfile_dlpolyplugin_fini(); \
+    molfile_dsn6plugin_fini(); \
+    molfile_dxplugin_fini(); \
+    molfile_edmplugin_fini(); \
+    molfile_fs4plugin_fini(); \
+    molfile_gamessplugin_fini(); \
+    molfile_graspplugin_fini(); \
+    molfile_grdplugin_fini(); \
+    molfile_gridplugin_fini(); \
+    molfile_gromacsplugin_fini(); \
+    molfile_jsplugin_fini(); \
+    molfile_lammpsplugin_fini(); \
+    molfile_mapplugin_fini(); \
+    molfile_mdfplugin_fini(); \
+    molfile_mol2plugin_fini(); \
+    molfile_moldenplugin_fini(); \
+    molfile_molemeshplugin_fini(); \
+    molfile_msmsplugin_fini(); \
+    molfile_namdbinplugin_fini(); \
+    molfile_offplugin_fini(); \
+    molfile_parm7plugin_fini(); \
+    molfile_parmplugin_fini(); \
+    molfile_pbeqplugin_fini(); \
+    molfile_pdbplugin_fini(); \
+    molfile_pdbxplugin_fini(); \
+    molfile_phiplugin_fini(); \
+    molfile_pltplugin_fini(); \
+    molfile_plyplugin_fini(); \
+    molfile_pqrplugin_fini(); \
+    molfile_psfplugin_fini(); \
+    molfile_raster3dplugin_fini(); \
+    molfile_rst7plugin_fini(); \
+    molfile_situsplugin_fini(); \
+    molfile_spiderplugin_fini(); \
+    molfile_stlplugin_fini(); \
+    molfile_tinkerplugin_fini(); \
+    molfile_uhbdplugin_fini(); \
+    molfile_vaspchgcarplugin_fini(); \
+    molfile_vaspoutcarplugin_fini(); \
+    molfile_vaspparchgplugin_fini(); \
+    molfile_vaspposcarplugin_fini(); \
+    molfile_vasp5xdatcarplugin_fini(); \
+    molfile_vaspxdatcarplugin_fini(); \
+    molfile_vaspxmlplugin_fini(); \
+    molfile_vtkplugin_fini(); \
+    molfile_xbgfplugin_fini(); \
+    molfile_xsfplugin_fini(); \
+    molfile_xyzplugin_fini(); \
+    molfile_dtrplugin_fini(); \
+    molfile_maeffplugin_fini(); \
+
+#ifdef __cplusplus
+}
+#endif
+#endif
--- a/plugins/MACOSXARM64/molfile/maeffplugin.so
+++ b/plugins/MACOSXARM64/molfile/maeffplugin.so
--- a/plugins/MACOSXARM64/molfile/mapplugin.so
+++ b/plugins/MACOSXARM64/molfile/mapplugin.so
--- a/plugins/MACOSXARM64/molfile/mdfplugin.so
+++ b/plugins/MACOSXARM64/molfile/mdfplugin.so
--- a/plugins/MACOSXARM64/molfile/mol2plugin.so
+++ b/plugins/MACOSXARM64/molfile/mol2plugin.so
--- a/plugins/MACOSXARM64/molfile/moldenplugin.so
+++ b/plugins/MACOSXARM64/molfile/moldenplugin.so
--- a/plugins/MACOSXARM64/molfile/molemeshplugin.so
+++ b/plugins/MACOSXARM64/molfile/molemeshplugin.so
--- a/plugins/MACOSXARM64/molfile/msmsplugin.so
+++ b/plugins/MACOSXARM64/molfile/msmsplugin.so
--- a/plugins/MACOSXARM64/molfile/namdbinplugin.so
+++ b/plugins/MACOSXARM64/molfile/namdbinplugin.so
--- a/plugins/MACOSXARM64/molfile/offplugin.so
+++ b/plugins/MACOSXARM64/molfile/offplugin.so
--- a/plugins/MACOSXARM64/molfile/parm7plugin.so
+++ b/plugins/MACOSXARM64/molfile/parm7plugin.so
--- a/plugins/MACOSXARM64/molfile/parmplugin.so
+++ b/plugins/MACOSXARM64/molfile/parmplugin.so
--- a/plugins/MACOSXARM64/molfile/pbeqplugin.so
+++ b/plugins/MACOSXARM64/molfile/pbeqplugin.so
--- a/plugins/MACOSXARM64/molfile/pdbplugin.so
+++ b/plugins/MACOSXARM64/molfile/pdbplugin.so
--- a/plugins/MACOSXARM64/molfile/pdbxplugin.so
+++ b/plugins/MACOSXARM64/molfile/pdbxplugin.so
--- a/plugins/MACOSXARM64/molfile/phiplugin.so
+++ b/plugins/MACOSXARM64/molfile/phiplugin.so
--- a/plugins/MACOSXARM64/molfile/pltplugin.so
+++ b/plugins/MACOSXARM64/molfile/pltplugin.so
--- a/plugins/MACOSXARM64/molfile/plyplugin.so
+++ b/plugins/MACOSXARM64/molfile/plyplugin.so
--- a/plugins/MACOSXARM64/molfile/pqrplugin.so
+++ b/plugins/MACOSXARM64/molfile/pqrplugin.so
--- a/plugins/MACOSXARM64/molfile/psfplugin.so
+++ b/plugins/MACOSXARM64/molfile/psfplugin.so
--- a/plugins/MACOSXARM64/molfile/raster3dplugin.so
+++ b/plugins/MACOSXARM64/molfile/raster3dplugin.so
--- a/plugins/MACOSXARM64/molfile/rst7plugin.so
+++ b/plugins/MACOSXARM64/molfile/rst7plugin.so
--- a/plugins/MACOSXARM64/molfile/situsplugin.so
+++ b/plugins/MACOSXARM64/molfile/situsplugin.so
--- a/plugins/MACOSXARM64/molfile/spiderplugin.so
+++ b/plugins/MACOSXARM64/molfile/spiderplugin.so
--- a/plugins/MACOSXARM64/molfile/stlplugin.so
+++ b/plugins/MACOSXARM64/molfile/stlplugin.so
--- a/plugins/MACOSXARM64/molfile/tinkerplugin.so
+++ b/plugins/MACOSXARM64/molfile/tinkerplugin.so
--- a/plugins/MACOSXARM64/molfile/uhbdplugin.so
+++ b/plugins/MACOSXARM64/molfile/uhbdplugin.so
--- a/plugins/MACOSXARM64/molfile/vasp5xdatcarplugin.so
+++ b/plugins/MACOSXARM64/molfile/vasp5xdatcarplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspchgcarplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspchgcarplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspoutcarplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspoutcarplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspparchgplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspparchgplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspposcarplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspposcarplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspxdatcarplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspxdatcarplugin.so
--- a/plugins/MACOSXARM64/molfile/vaspxmlplugin.so
+++ b/plugins/MACOSXARM64/molfile/vaspxmlplugin.so
--- a/plugins/MACOSXARM64/molfile/vtkplugin.so
+++ b/plugins/MACOSXARM64/molfile/vtkplugin.so
--- a/plugins/MACOSXARM64/molfile/xbgfplugin.so
+++ b/plugins/MACOSXARM64/molfile/xbgfplugin.so
--- a/plugins/MACOSXARM64/molfile/xsfplugin.so
+++ b/plugins/MACOSXARM64/molfile/xsfplugin.so
--- a/plugins/MACOSXARM64/molfile/xyzplugin.so
+++ b/plugins/MACOSXARM64/molfile/xyzplugin.so
--- a/src/pertable.c
+++ b/src/pertable.c
@@ -260,11 +260,13 @@ float pte_get_enegativity(const char *symbol)
 */
 char *pte_get_element_from_number(int atomicnumber)
 {
+	
 	char *tmp=malloc(sizeof(char)*3) ;
 	if(atomicnumber>0 && atomicnumber<112){
 	
 		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
 		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
+		tmp[2]='\0';
 		return tmp;
 	} else {
 		tmp[0]='-';
--- a/src/read_mmcif.c
+++ b/src/read_mmcif.c
@@ -63,7 +63,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
    void *h_in;
    molfile_timestep_t ts_in;
    molfile_atom_t *at_in;
-    int optflags = 0x0040;
+    int optflags[] = {0x0001,0x0040};
    int rc;
    int rc2;
    int j;
@@ -75,7 +75,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
    }
    at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
    ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
-    rc2 = api->read_structure(h_in, &optflags, at_in);
+    rc2 = api->read_structure(h_in, optflags, at_in);
    rc = api->read_next_timestep(h_in, inatoms, &ts_in);
    if (!model_number)
        model_number = 1;
@@ -124,7 +124,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
            if (par->xlig_resnumber > -1)
            {

-                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
                {
                    pdb->n_xlig_atoms++;
                }
@@ -179,7 +179,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
            }
            if (par->xlig_resnumber > -1)
            {   
-                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid_auth == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
                {
                    pdb->n_xlig_atoms++;
                }
@@ -314,7 +314,9 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                            atom->pdb_aloc = at_in[i].altloc[0];
                            strcpy(atom->res_name, at_in[i].resname);
                            strcpy(atom->chain, at_in[i].chain_auth);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                            atom->pdb_insert = at_in[i].insertion[0];
                            atom->x = ts_in.coords[(3 * i)];
                            atom->y = ts_in.coords[(3 * i) + 1];
@@ -351,7 +353,9 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                            atom->pdb_aloc = at_in[i].altloc[0];
                            strcpy(atom->res_name, at_in[i].resname);
                            strcpy(atom->chain, at_in[i].chain_auth);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                            atom->pdb_insert = at_in[i].insertion[0];
                            atom->x = ts_in.coords[(3 * i)];
                            atom->y = ts_in.coords[(3 * i) + 1];
@@ -396,7 +400,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                        strcpy(atom->res_name, at_in[i].resname);

                        strcpy(atom->chain, at_in[i].chain_auth);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                        atom->pdb_insert = at_in[i].insertion[0];

                        atom->x = ts_in.coords[(3 * i)];
@@ -429,7 +436,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
            {
                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));

-                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
                {
                    *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                    *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
@@ -466,8 +473,11 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                        atom->pdb_aloc = at_in[i].altloc[0];
                        strcpy(atom->res_name, at_in[i].resname);
                        strcpy(atom->chain, at_in[i].chain_auth);
-                        atom->res_id = at_in[i].resid;
+                        strcpy(atom->label_asym_id, at_in[i].chain);
+                        atom->res_id = at_in[i].resid_auth;
+                        atom->label_seq_id=at_in[i].resid;
                        atom->pdb_insert = at_in[i].insertion[0];
+
                        atom->x = ts_in.coords[(3 * i)];
                        atom->y = ts_in.coords[(3 * i) + 1];
                        atom->z = ts_in.coords[(3 * i) + 2];
@@ -503,7 +513,9 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                            atom->pdb_aloc = at_in[i].altloc[0];
                            strcpy(atom->res_name, at_in[i].resname);
                            strcpy(atom->chain, at_in[i].chain_auth);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                            atom->pdb_insert = at_in[i].insertion[0];
                            atom->x = ts_in.coords[(3 * i)];
                            atom->y = ts_in.coords[(3 * i) + 1];
@@ -541,8 +553,11 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                            atom->pdb_aloc = at_in[i].altloc[0];
                            strcpy(atom->res_name, at_in[i].resname);
                            strcpy(atom->chain, at_in[i].chain_auth);
-                            atom->res_id = at_in[i].resid;
+                            strcpy(atom->label_asym_id, at_in[i].chain);
+                            atom->res_id = at_in[i].resid_auth;
+                            atom->label_seq_id=at_in[i].resid;
                            atom->pdb_insert = at_in[i].insertion[0];
+
                            atom->x = ts_in.coords[(3 * i)];
                            atom->y = ts_in.coords[(3 * i) + 1];
                            atom->z = ts_in.coords[(3 * i) + 2];
@@ -579,7 +594,9 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                    atom->pdb_aloc = at_in[i].altloc[0];
                                    strcpy(atom->res_name, at_in[i].resname);
                                    strcpy(atom->chain, at_in[i].chain_auth);
-                                    atom->res_id = at_in[i].resid;
+                                    strcpy(atom->label_asym_id, at_in[i].chain);
+                                    atom->res_id = at_in[i].resid_auth;
+                                    atom->label_seq_id=at_in[i].resid;
                                    atom->pdb_insert = at_in[i].insertion[0];
                                    atom->x = ts_in.coords[(3 * i)];
                                    atom->y = ts_in.coords[(3 * i) + 1];
@@ -607,13 +624,13 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                    }
                }
            }
-
+                                                         
            if (pdb->n_xlig_atoms)
            {

                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));

-                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
                {
                                        
                    *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
--- a/src/rpdb.c
+++ b/src/rpdb.c
@@ -1161,6 +1161,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                atom->radius = pte_get_vdw_ray(atom->symbol);
                                atom->electroneg = pte_get_enegativity(atom->symbol);
                                atom->sort_x = -1;
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+

                                atoms_p[iatoms] = atom;
                                iatoms++;
@@ -1189,7 +1192,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                atom->radius = pte_get_vdw_ray(atom->symbol);
                                atom->electroneg = pte_get_enegativity(atom->symbol);
                                atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                atoms_p[iatoms] = atom;
                                iatoms++;

@@ -1215,6 +1220,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                            atom->radius = pte_get_vdw_ray(atom->symbol);
                            atom->electroneg = pte_get_enegativity(atom->symbol);
                            atom->sort_x = -1;
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                            // printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain  : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
                            // atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
                            // printf("electroneg : %s\n",atom->symbol);
@@ -1284,7 +1292,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                            atom->radius = pte_get_vdw_ray(atom->symbol);
                            atom->electroneg = pte_get_enegativity(atom->symbol);
                            atom->sort_x = -1;
-
+                            atom->label_seq_id=atom->res_id;
+                            strcpy(atom->label_asym_id, atom->chain);
+                                
                            atoms_p[iatoms] = atom;
                            atm_lig[iatm_lig] = atom;

@@ -1310,7 +1320,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                atom->radius = pte_get_vdw_ray(atom->symbol);
                                atom->electroneg = pte_get_enegativity(atom->symbol);
                                atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                atoms_p[iatoms] = atom;
                                atm_lig[iatm_lig] = atom;

@@ -1338,7 +1350,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                atom->radius = pte_get_vdw_ray(atom->symbol);
                                atom->electroneg = pte_get_enegativity(atom->symbol);
                                atom->sort_x = -1;
-
+                                atom->label_seq_id=atom->res_id;
+                                strcpy(atom->label_asym_id, atom->chain);
+                                
                                atoms_p[iatoms] = atom;
                                pdb->lhetatm[ihetatm] = atom;
                                ihetatm++;
@@ -1366,7 +1380,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                        atom->radius = pte_get_vdw_ray(atom->symbol);
                                        atom->electroneg = pte_get_enegativity(atom->symbol);
                                        atom->sort_x = -1;
-
+                                        atom->label_seq_id=atom->res_id;
+                                        strcpy(atom->label_asym_id, atom->chain);
+                                
                                        atoms_p[iatoms] = atom;
                                        pdb->lhetatm[ihetatm] = atom;
                                        ihetatm++;
--- a/src/voronoi.c
+++ b/src/voronoi.c
@@ -1488,23 +1488,23 @@ void write_mmcif_vert(FILE *f, s_vvertice *v, int i)
    if (v->electrostatic_energy <= -0.05)
    {

-        write_mmcif_atom_line(f, "HETATM", i, " POL",
-                              ' ', "ACC", "O", v->resid, ' ',
+        write_mmcif_atom_line(f, "HETATM", i, "POL",
+                              '.', "ACC", "O", v->resid, "O",v->resid,'.',
                              v->x, v->y, v->z, 0.0, 0.0, 0,
                              "V", -1, 0.0);
    }
    else if (v->electrostatic_energy >= 0.05)
    {

-        write_mmcif_atom_line(f, "HETATM", i, " POL", ' ', "DON", "N",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "POL", '.', "DON", "N",
+                              v->resid, "N",v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                              "V", -1, 0.0);
    }
    else
    {

-        write_mmcif_atom_line(f, "HETATM", i, "APOL", ' ', "STP", "C",
-                              v->resid, ' ', v->x, v->y, v->z, 0.0, 0.0, 0,
+        write_mmcif_atom_line(f, "HETATM", i, "APOL", '.', "STP", "C",
+                              v->resid, "C", v->resid,'.', v->x, v->y, v->z, 0.0, 0.0, 0,
                              "V", -1, 0.0);
    }
 }
--- a/src/writepdb.c
+++ b/src/writepdb.c
@@ -206,7 +206,7 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom

 void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
 						   char alt_loc, const char res_name[], const char chain[],
-						   int res_id, const char insert, float x, float y, float z, float occ,
+						   int res_id, const char label_asym_id[],int label_seq_id, char insert, float x, float y, float z, float occ,
 						   float bfactor, int abpa, const char *symbol, int charge, float abpa_prob)
 {
 	int status = 0;
@@ -214,19 +214,13 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 		 res_id_buf[5] = "****",
 		 charge_buf[3] = "  \0";

-	if (id < 100000)
-		sprintf(id_buf, "%5d", id);
-	else
-		sprintf(id_buf, "%05x", id);
+	
+	sprintf(id_buf, "%d", id);
+	
+	sprintf(res_id_buf, "%d", res_id);

-	if (res_id < 10000)
-		sprintf(res_id_buf, "%4d", res_id);
-	else if (res_id < 65536)
-		sprintf(res_id_buf, "%04x", res_id);
-	else
-		sprintf(res_id_buf, "****");
-
-	alt_loc = (alt_loc == '\0') ? ' ' : alt_loc;
+	alt_loc = (alt_loc == '\0' || (alt_loc == ' '))  ? '?' : alt_loc;
+	insert = (insert == '\0' || insert==' ') ? '?' : insert;

 	if (charge == -1)
 		sprintf(charge_buf, " 0");
@@ -237,14 +231,8 @@ void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char at
 	if (abpa)
 		finalabpa = abpa_prob;

-	//status = fprintf(f, "%-7s %6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s %4s %4s %2s %4s\n",
-	//				 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, res_id_buf, res_name, chain, atom_name);
+	status = fprintf(f, "%-7s %-6s %3s %4s %c %4s %6s %d %c %8.3f %8.3f %8.3f %6.2f %2s %d %s\n",
+					 rec_name, id_buf, symbol, atom_name,alt_loc, res_name, label_asym_id, label_seq_id,insert, x, y, z, occ, charge_buf, res_id,chain);

-	status = fprintf(f, "%-7s %-6s %3s %4s . %4s %3s . %s ? %8.3f%8.3f%8.3f%6.2f %2s  %2s\n",
-					 rec_name, id_buf, symbol, atom_name, res_name, chain, res_id_buf, x, y, z, occ, charge_buf, chain);
+}

-	/*"ATOM %d %s %s . %s %s . %d ? %f %f %f %f %f %s\n",
-            i + 1, atoms[i].name, atoms[i].type, atoms[i].resname, atoms[i].chain,
-            atoms[i].resid, *x, *y, *z, atoms[i].occupancy,
-            atoms[i].charge, atoms[i].chain);*/
-}
--- a/src/writepocket.c
+++ b/src/writepocket.c
@@ -44,7 +44,6 @@ static const char atomSiteHeader[] =
    "_atom_site.label_alt_id\n"
    "_atom_site.label_comp_id\n"
    "_atom_site.label_asym_id\n"
-    "_atom_site.label_entity_id\n"
    "_atom_site.label_seq_id\n"
    "_atom_site.pdbx_PDB_ins_code\n"
    "_atom_site.Cartn_x\n"
@@ -52,6 +51,7 @@ static const char atomSiteHeader[] =
    "_atom_site.Cartn_z\n"
    "_atom_site.occupancy\n"
    "_atom_site.pdbx_formal_charge\n"
+    "_atom_site.auth_seq_id\n"
    "_atom_site.auth_asym_id\n";

    /*static const char atomSiteHeader[] =
@@ -214,7 +214,7 @@ void write_pocket_mmcif_DB(const char out[], s_pocket *pocket, s_pdb *pdb) {
        for (i = 0; i < n_sa; i++) {
            atom = pdb->latoms_p[sa[i]];
            write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                    atom->res_name, atom->chain, atom->res_id,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
                    atom->pdb_insert, atom->x, atom->y, atom->z,
                    atom->dA, atom->a0, atom->abpa, atom->symbol,
                    atom->charge, atom->abpa_sourrounding_prob);
@@ -375,9 +375,9 @@ void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms) {
    for (i = 0; i < natoms; i++) {
        atom = atoms + i;
        //atom->chain[1]='\0';
-        //printf("%d:%s|symb:%s\t",i,atom->chain,atom->symbol);
+        // printf("%d:%s vs %s\n",i,atom->chain,atom->label_asym_id);
        write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                atom->res_name, atom->chain, atom->res_id,
+                atom->res_name, atom->chain,atom->res_id,atom->label_asym_id,atom->label_seq_id,
                atom->pdb_insert, atom->x, atom->y, atom->z,
                atom->dA, atom->a0, atom->abpa, atom->symbol,
                atom->charge, atom->abpa_sourrounding_prob);
@@ -742,7 +742,7 @@ void write_pocket_mmcif(const char out[], s_pocket *pocket) {
            atom = atms[i];

            write_mmcif_atom_line(f, atom->type, atom->id, atom->name, atom->pdb_aloc,
-                    atom->res_name, atom->chain, atom->res_id,
+                    atom->res_name, atom->chain, atom->res_id,atom->label_asym_id,atom->label_seq_id,
                    atom->pdb_insert, atom->x, atom->y, atom->z,
                    atom->dA, atom->a0, atom->abpa, atom->symbol,
                    atom->charge, atom->abpa_sourrounding_prob);
--- a/tests/reference_output/123abc_out/pocket10_atm.cif
+++ b/tests/reference_output/123abc_out/pocket10_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    10:
 6  - Hydrophobicity Score              : 40.0769
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 3.6154
-9  - Pocket volume (Monte Carlo)       : 433.6981
+9  - Pocket volume (Monte Carlo)       : 433.1334
 10  -Pocket volume (convex hull)       : 76.0139
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 32.4571
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,39 +37,40 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3335    C  CG2 .  THR   B .  167 ?   23.611  41.302  32.855  0.00  0   B
-ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
-ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
-ATOM     3399    C  CD1 .  ILE   B .  176 ?   22.413  39.457  35.570  0.00  0   B
-ATOM     3397    C  CG1 .  ILE   B .  176 ?   21.483  40.079  36.568  0.00  0   B
-ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
-ATOM     3378    C   CB .  PHE   B .  174 ?   18.390  43.943  35.478  0.00  0   B
-ATOM     3332    O    O .  THR   B .  167 ?   21.633  44.211  32.694 -1.07  0   B
-ATOM     3735    C   CA .  SER   B .  219 ?   24.536  33.701  35.059  0.00  0   B
-ATOM     3729    O    O .  LEU   B .  218 ?   23.720  35.415  36.830  0.00  0   B
-ATOM     1239    C   CB .  ALA   A .  168 ?   21.952  31.542  32.252  0.00  0   A
-ATOM     3454    O    O .  SER   B .  183 ?   12.618  40.049  35.823 -1.07  0   B
-ATOM     3488    O  OD1 .  ASN   B .  187 ?   12.383  40.631  32.241 -1.07  0   B
-ATOM     3380    C  CD1 .  PHE   B .  174 ?   16.492  43.534  33.887  0.00  0   B
-ATOM     3460    O    O .  LEU   B .  184 ?   14.089  37.175  34.255 -3.21  0   B
-ATOM     3458    C   CA .  LEU   B .  184 ?   14.473  38.083  36.400  0.00  0   B
-ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
-ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
-ATOM     3760    C   CB .  TYR   B .  222 ?   18.259  32.959  38.062  0.00  0   B
-ATOM     3756    N    N .  TYR   B .  222 ?   20.251  33.164  39.466 -1.09  0   B
-ATOM     3398    C  CG2 .  ILE   B .  176 ?   21.928  38.594  38.565  0.00  0   B
-ATOM     3463    C  CD1 .  LEU   B .  184 ?   17.369  37.208  38.932  0.00  0   B
-ATOM     3737    O    O .  SER   B .  219 ?   23.395  31.686  35.276 -1.07  0   B
-ATOM     3728    C    C .  LEU   B .  218 ?   24.912  35.395  36.613  0.00  0   B
-ATOM     3730    C   CB .  LEU   B .  218 ?   25.994  37.693  36.437  0.00  0   B
-ATOM     3738    C   CB .  SER   B .  219 ?   25.152  33.376  33.704  0.00  0   B
-ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
-ATOM     3464    C  CD2 .  LEU   B .  184 ?   17.512  38.953  37.066  0.00  0   B
-ATOM     3734    N    N .  SER   B .  219 ?   25.438  34.466  35.848 -1.09  0   B
-ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
-ATOM     3461    C   CB .  LEU   B .  184 ?   15.552  37.271  37.155  0.00  0   B
-ATOM     1250    N    N .  ALA   A .  170 ?   17.224  33.325  33.516 -4.79  0   A
-ATOM     1255    N    N .  GLY   A .  171 ?   17.151  30.558  34.884 -1.09  0   A
-ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
+ATOM    3335     C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    3399     C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM    3397     C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3378     C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM    3332     O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM    3735     C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM    3729     O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM    1239     C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM    3454     O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM    3488     O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM    3380     C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM    3460     O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM    3458     C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    3760     C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM    3756     N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM    3398     C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM    3463     C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM    3737     O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM    3728     C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM    3730     C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM    3738     C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3464     C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM    3734     N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    3461     C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM    1250     N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM    1255     N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
 # 
--- a/tests/reference_output/123abc_out/pocket10_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket10_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,76 +15,77 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     1236    C   CA .  ALA   A .  168 ?   21.345  31.742  30.855  0.00  0   A
-ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
-ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
-ATOM     1239    C   CB .  ALA   A .  168 ?   21.952  31.542  32.252  0.00  0   A
-ATOM     1240    N    N .  HIS   A .  169 ?   19.130  32.633  31.043  0.00  0   A
-ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
-ATOM     1242    C    C .  HIS   A .  169 ?   17.124  32.937  32.241  0.00  0   A
-ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
-ATOM     1245    C   CG .  HIS   A .  169 ?   16.104  34.797  30.229  0.00  0   A
-ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
-ATOM     1249    N  NE2 .  HIS   A .  169 ?   14.590  36.367  30.529  0.00  0   A
-ATOM     1250    N    N .  ALA   A .  170 ?   17.224  33.325  33.516 -4.79  0   A
-ATOM     1251    C   CA .  ALA   A .  170 ?   16.342  32.830  34.571  0.00  0   A
-ATOM     1252    C    C .  ALA   A .  170 ?   16.105  31.311  34.539  0.00  0   A
-ATOM     1254    C   CB .  ALA   A .  170 ?   15.038  33.564  34.528  0.00  0   A
-ATOM     1255    N    N .  GLY   A .  171 ?   17.151  30.558  34.884 -1.09  0   A
-ATOM     3331    C    C .  THR   B .  167 ?   22.771  43.904  32.327  0.00  0   B
-ATOM     3332    O    O .  THR   B .  167 ?   21.633  44.211  32.694 -1.07  0   B
-ATOM     3333    C   CB .  THR   B .  167 ?   23.958  42.338  33.911  0.00  0   B
-ATOM     3335    C  CG2 .  THR   B .  167 ?   23.611  41.302  32.855  0.00  0   B
-ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
-ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
-ATOM     3341    N    N .  HIS   B .  169 ?   19.743  43.280  29.949  0.00  0   B
-ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
-ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
-ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
-ATOM     3347    N  ND1 .  HIS   B .  169 ?   15.399  41.864  29.978 -2.19  0   B
-ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
-ATOM     3349    C  CE1 .  HIS   B .  169 ?   14.459  40.980  29.690  0.00  0   B
-ATOM     3350    N  NE2 .  HIS   B .  169 ?   14.959  39.769  29.859  0.00  0   B
-ATOM     3374    N    N .  PHE   B .  174 ?   19.806  45.500  34.237  0.00  0   B
-ATOM     3375    C   CA .  PHE   B .  174 ?   19.360  45.109  35.564  0.00  0   B
-ATOM     3377    O    O .  PHE   B .  174 ?   21.500  44.304  36.088  0.00  0   B
-ATOM     3378    C   CB .  PHE   B .  174 ?   18.390  43.943  35.478  0.00  0   B
-ATOM     3379    C   CG .  PHE   B .  174 ?   17.076  44.325  34.855  0.00  0   B
-ATOM     3380    C  CD1 .  PHE   B .  174 ?   16.492  43.534  33.887  0.00  0   B
-ATOM     3382    C  CE1 .  PHE   B .  174 ?   15.273  43.909  33.319  0.00  0   B
-ATOM     3396    C   CB .  ILE   B .  176 ?   21.966  39.989  38.044  0.00  0   B
-ATOM     3397    C  CG1 .  ILE   B .  176 ?   21.483  40.079  36.568  0.00  0   B
-ATOM     3398    C  CG2 .  ILE   B .  176 ?   21.928  38.594  38.565  0.00  0   B
-ATOM     3399    C  CD1 .  ILE   B .  176 ?   22.413  39.457  35.570  0.00  0   B
-ATOM     3453    C    C .  SER   B .  183 ?   12.616  39.571  36.930  0.00  0   B
-ATOM     3454    O    O .  SER   B .  183 ?   12.618  40.049  35.823 -1.07  0   B
-ATOM     3457    N    N .  LEU   B .  184 ?   13.478  38.624  37.304  0.00  0   B
-ATOM     3458    C   CA .  LEU   B .  184 ?   14.473  38.083  36.400  0.00  0   B
-ATOM     3459    C    C .  LEU   B .  184 ?   13.764  37.165  35.433  0.00  0   B
-ATOM     3460    O    O .  LEU   B .  184 ?   14.089  37.175  34.255 -3.21  0   B
-ATOM     3461    C   CB .  LEU   B .  184 ?   15.552  37.271  37.155  0.00  0   B
-ATOM     3462    C   CG .  LEU   B .  184 ?   16.587  38.098  37.951  0.00  0   B
-ATOM     3463    C  CD1 .  LEU   B .  184 ?   17.369  37.208  38.932  0.00  0   B
-ATOM     3464    C  CD2 .  LEU   B .  184 ?   17.512  38.953  37.066  0.00  0   B
-ATOM     3488    O  OD1 .  ASN   B .  187 ?   12.383  40.631  32.241 -1.07  0   B
-ATOM     3727    C   CA .  LEU   B .  218 ?   25.851  36.423  37.264  0.00  0   B
-ATOM     3728    C    C .  LEU   B .  218 ?   24.912  35.395  36.613  0.00  0   B
-ATOM     3729    O    O .  LEU   B .  218 ?   23.720  35.415  36.830  0.00  0   B
-ATOM     3730    C   CB .  LEU   B .  218 ?   25.994  37.693  36.437  0.00  0   B
-ATOM     3734    N    N .  SER   B .  219 ?   25.438  34.466  35.848 -1.09  0   B
-ATOM     3735    C   CA .  SER   B .  219 ?   24.536  33.701  35.059  0.00  0   B
-ATOM     3736    C    C .  SER   B .  219 ?   24.150  32.474  35.811  0.00  0   B
-ATOM     3737    O    O .  SER   B .  219 ?   23.395  31.686  35.276 -1.07  0   B
-ATOM     3738    C   CB .  SER   B .  219 ?   25.152  33.376  33.704  0.00  0   B
-ATOM     3751    C    C .  VAL   B .  221 ?   21.031  32.982  40.538  0.00  0   B
-ATOM     3753    C   CB .  VAL   B .  221 ?   22.559  35.077  40.397  0.00  0   B
-ATOM     3756    N    N .  TYR   B .  222 ?   20.251  33.164  39.466 -1.09  0   B
-ATOM     3757    C   CA .  TYR   B .  222 ?   18.886  32.708  39.432  0.00  0   B
-ATOM     3760    C   CB .  TYR   B .  222 ?   18.259  32.959  38.062  0.00  0   B
-ATOM     3761    C   CG .  TYR   B .  222 ?   16.811  32.522  38.032  0.00  0   B
-ATOM     3762    C  CD1 .  TYR   B .  222 ?   15.795  33.459  38.329  0.00  0   B
-ATOM     3768    N    N .  GLU   B .  223 ?   19.652  30.471  39.123  0.00  0   B
-ATOM     3773    C   CG .  GLU   B .  223 ?   20.865  28.953  37.013  0.00  0   B
-ATOM     3776    O  OE2 .  GLU   B .  223 ?   21.549  28.266  34.820  0.00  0   B
+ATOM    1236     C   CA ?  ALA    Axp 168 ?   21.345   31.742   30.855   0.00  0 395 A
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    1239     C   CB ?  ALA    Axp 168 ?   21.952   31.542   32.252   0.00  0 395 A
+ATOM    1240     N    N ?  HIS    Axp 169 ?   19.130   32.633   31.043   0.00  0 396 A
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    1242     C    C ?  HIS    Axp 169 ?   17.124   32.937   32.241   0.00  0 396 A
+ATOM    1244     C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM    1245     C   CG ?  HIS    Axp 169 ?   16.104   34.797   30.229   0.00  0 396 A
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    1249     N  NE2 ?  HIS    Axp 169 ?   14.590   36.367   30.529   0.00  0 396 A
+ATOM    1250     N    N ?  ALA    Axp 170 ?   17.224   33.325   33.516  -4.79  0 397 A
+ATOM    1251     C   CA ?  ALA    Axp 170 ?   16.342   32.830   34.571   0.00  0 397 A
+ATOM    1252     C    C ?  ALA    Axp 170 ?   16.105   31.311   34.539   0.00  0 397 A
+ATOM    1254     C   CB ?  ALA    Axp 170 ?   15.038   33.564   34.528   0.00  0 397 A
+ATOM    1255     N    N ?  GLY    Axp 171 ?   17.151   30.558   34.884  -1.09  0 398 A
+ATOM    3331     C    C ?  THR    Bxp 167 ?   22.771   43.904   32.327   0.00  0 394 B
+ATOM    3332     O    O ?  THR    Bxp 167 ?   21.633   44.211   32.694  -1.07  0 394 B
+ATOM    3333     C   CB ?  THR    Bxp 167 ?   23.958   42.338   33.911   0.00  0 394 B
+ATOM    3335     C  CG2 ?  THR    Bxp 167 ?   23.611   41.302   32.855   0.00  0 394 B
+ATOM    3338     C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    3341     N    N ?  HIS    Bxp 169 ?   19.743   43.280   29.949   0.00  0 396 B
+ATOM    3342     C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3347     N  ND1 ?  HIS    Bxp 169 ?   15.399   41.864   29.978  -2.19  0 396 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    3349     C  CE1 ?  HIS    Bxp 169 ?   14.459   40.980   29.690   0.00  0 396 B
+ATOM    3350     N  NE2 ?  HIS    Bxp 169 ?   14.959   39.769   29.859   0.00  0 396 B
+ATOM    3374     N    N ?  PHE    Bxp 174 ?   19.806   45.500   34.237   0.00  0 401 B
+ATOM    3375     C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM    3377     O    O ?  PHE    Bxp 174 ?   21.500   44.304   36.088   0.00  0 401 B
+ATOM    3378     C   CB ?  PHE    Bxp 174 ?   18.390   43.943   35.478   0.00  0 401 B
+ATOM    3379     C   CG ?  PHE    Bxp 174 ?   17.076   44.325   34.855   0.00  0 401 B
+ATOM    3380     C  CD1 ?  PHE    Bxp 174 ?   16.492   43.534   33.887   0.00  0 401 B
+ATOM    3382     C  CE1 ?  PHE    Bxp 174 ?   15.273   43.909   33.319   0.00  0 401 B
+ATOM    3396     C   CB ?  ILE    Bxp 176 ?   21.966   39.989   38.044   0.00  0 403 B
+ATOM    3397     C  CG1 ?  ILE    Bxp 176 ?   21.483   40.079   36.568   0.00  0 403 B
+ATOM    3398     C  CG2 ?  ILE    Bxp 176 ?   21.928   38.594   38.565   0.00  0 403 B
+ATOM    3399     C  CD1 ?  ILE    Bxp 176 ?   22.413   39.457   35.570   0.00  0 403 B
+ATOM    3453     C    C ?  SER    Bxp 183 ?   12.616   39.571   36.930   0.00  0 410 B
+ATOM    3454     O    O ?  SER    Bxp 183 ?   12.618   40.049   35.823  -1.07  0 410 B
+ATOM    3457     N    N ?  LEU    Bxp 184 ?   13.478   38.624   37.304   0.00  0 411 B
+ATOM    3458     C   CA ?  LEU    Bxp 184 ?   14.473   38.083   36.400   0.00  0 411 B
+ATOM    3459     C    C ?  LEU    Bxp 184 ?   13.764   37.165   35.433   0.00  0 411 B
+ATOM    3460     O    O ?  LEU    Bxp 184 ?   14.089   37.175   34.255  -3.21  0 411 B
+ATOM    3461     C   CB ?  LEU    Bxp 184 ?   15.552   37.271   37.155   0.00  0 411 B
+ATOM    3462     C   CG ?  LEU    Bxp 184 ?   16.587   38.098   37.951   0.00  0 411 B
+ATOM    3463     C  CD1 ?  LEU    Bxp 184 ?   17.369   37.208   38.932   0.00  0 411 B
+ATOM    3464     C  CD2 ?  LEU    Bxp 184 ?   17.512   38.953   37.066   0.00  0 411 B
+ATOM    3488     O  OD1 ?  ASN    Bxp 187 ?   12.383   40.631   32.241  -1.07  0 414 B
+ATOM    3727     C   CA ?  LEU    Bxp 218 ?   25.851   36.423   37.264   0.00  0 445 B
+ATOM    3728     C    C ?  LEU    Bxp 218 ?   24.912   35.395   36.613   0.00  0 445 B
+ATOM    3729     O    O ?  LEU    Bxp 218 ?   23.720   35.415   36.830   0.00  0 445 B
+ATOM    3730     C   CB ?  LEU    Bxp 218 ?   25.994   37.693   36.437   0.00  0 445 B
+ATOM    3734     N    N ?  SER    Bxp 219 ?   25.438   34.466   35.848  -1.09  0 446 B
+ATOM    3735     C   CA ?  SER    Bxp 219 ?   24.536   33.701   35.059   0.00  0 446 B
+ATOM    3736     C    C ?  SER    Bxp 219 ?   24.150   32.474   35.811   0.00  0 446 B
+ATOM    3737     O    O ?  SER    Bxp 219 ?   23.395   31.686   35.276  -1.07  0 446 B
+ATOM    3738     C   CB ?  SER    Bxp 219 ?   25.152   33.376   33.704   0.00  0 446 B
+ATOM    3751     C    C ?  VAL    Bxp 221 ?   21.031   32.982   40.538   0.00  0 448 B
+ATOM    3753     C   CB ?  VAL    Bxp 221 ?   22.559   35.077   40.397   0.00  0 448 B
+ATOM    3756     N    N ?  TYR    Bxp 222 ?   20.251   33.164   39.466  -1.09  0 449 B
+ATOM    3757     C   CA ?  TYR    Bxp 222 ?   18.886   32.708   39.432   0.00  0 449 B
+ATOM    3760     C   CB ?  TYR    Bxp 222 ?   18.259   32.959   38.062   0.00  0 449 B
+ATOM    3761     C   CG ?  TYR    Bxp 222 ?   16.811   32.522   38.032   0.00  0 449 B
+ATOM    3762     C  CD1 ?  TYR    Bxp 222 ?   15.795   33.459   38.329   0.00  0 449 B
+ATOM    3768     N    N ?  GLU    Bxp 223 ?   19.652   30.471   39.123   0.00  0 450 B
+ATOM    3773     C   CG ?  GLU    Bxp 223 ?   20.865   28.953   37.013   0.00  0 450 B
+ATOM    3776     O  OE2 ?  GLU    Bxp 223 ?   21.549   28.266   34.820   0.00  0 450 B
 #
--- a/tests/reference_output/123abc_out/pocket11_atm.cif
+++ b/tests/reference_output/123abc_out/pocket11_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    11:
 6  - Hydrophobicity Score              : 17.4167
 7  - Polarity Score                    :     7
 8  - Amino Acid based volume Score     : 3.8333
-9  - Pocket volume (Monte Carlo)       : 155.2499
+9  - Pocket volume (Monte Carlo)       : 157.8834
 10  -Pocket volume (convex hull)       : 11.3291
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 5.0000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,26 +37,27 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     1405    C  CD2 .  PHE   A .  189 ?   10.703  31.452  22.157  0.00  0   A
-ATOM     1435    O    O .  SER   A .  193 ?   11.879  32.960  15.552 -3.21  0   A
-ATOM     1407    C  CE2 .  PHE   A .  189 ?   11.966  31.656  22.739  0.00  0   A
-ATOM      996    O    O .  ARG   A .  135 ?   13.454  28.096  20.320 -4.69  0   A
-ATOM     1436    C   CB .  SER   A .  193 ?    9.997  34.149  17.982  0.00  0   A
-ATOM     1329    N    N .  ALA   A .  180 ?   14.229  35.929  18.757 -1.09  0   A
-ATOM     1327    O  OG1 .  THR   A .  179 ?   17.108  33.330  21.134 -2.14  0   A
-ATOM     1290    C   CD .  PRO   A .  175 ?   18.295  29.738  22.438  0.00  0   A
-ATOM     1323    C   CA .  THR   A .  179 ?   16.193  34.623  19.411  0.00  0   A
-ATOM     1437    O   OG .  SER   A .  193 ?    9.317  33.077  18.605  0.00  0   A
-ATOM     1289    C   CG .  PRO   A .  175 ?   18.737  29.443  21.033  0.00  0   A
-ATOM     1312    C   CB .  TRP   A .  178 ?   18.807  31.481  17.128  0.00  0   A
-ATOM     1005    C   CA .  ASP   A .  136 ?   14.988  26.627  18.681  0.00  0   A
-ATOM     1311    O    O .  TRP   A .  178 ?   16.495  33.261  16.896 -2.14  0   A
-ATOM     1471    C   CB .  ALA   A .  197 ?   14.926  31.065  14.885  0.00  0   A
-ATOM     1355    O   OG .  SER   A .  183 ?   10.954  35.267  20.964  0.00  0   A
-ATOM     1012    N    N .  LEU   A .  137 ?   14.970  26.942  16.300  0.00  0   A
-ATOM     1444    O  OD1 .  ASP   A .  194 ?   10.115  28.834  16.531  0.00  0   A
-ATOM      995    C    C .  ARG   A .  135 ?   12.856  27.406  19.519  0.00  0   A
-ATOM      994    C   CA .  ARG   A .  135 ?   11.309  27.407  19.509  0.00  0   A
-ATOM     1328    C  CG2 .  THR   A .  179 ?   15.235  34.657  21.794  0.00  0   A
+ATOM    1405     C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM    1435     O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM    1407     C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM    996      O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM    1436     C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM    1329     N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM    1327     O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM    1290     C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM    1323     C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM    1437     O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM    1289     C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM    1312     C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM    1005     C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM    1311     O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM    1471     C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
+ATOM    1355     O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM    1012     N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM    1444     O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM    995      C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM    994      C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM    1328     C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
 # 
--- a/tests/reference_output/123abc_out/pocket11_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket11_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,49 +15,50 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM      993    N    N .  ARG   A .  135 ?   10.598  26.723  18.417  0.00  0   A
-ATOM      994    C   CA .  ARG   A .  135 ?   11.309  27.407  19.509  0.00  0   A
-ATOM      995    C    C .  ARG   A .  135 ?   12.856  27.406  19.519  0.00  0   A
-ATOM      996    O    O .  ARG   A .  135 ?   13.454  28.096  20.320 -4.69  0   A
-ATOM      997    C   CB .  ARG   A .  135 ?   10.850  26.919  20.881  0.00  0   A
-ATOM     1004    N    N .  ASP   A .  136 ?   13.515  26.641  18.666  0.00  0   A
-ATOM     1005    C   CA .  ASP   A .  136 ?   14.988  26.627  18.681  0.00  0   A
-ATOM     1006    C    C .  ASP   A .  136 ?   15.413  26.185  17.291  0.00  0   A
-ATOM     1008    C   CB .  ASP   A .  136 ?   15.490  25.673  19.755  0.00  0   A
-ATOM     1009    C   CG .  ASP   A .  136 ?   16.996  25.759  19.996  0.00  0   A
-ATOM     1010    O  OD1 .  ASP   A .  136 ?   17.712  26.739  19.639  0.00  0   A
-ATOM     1012    N    N .  LEU   A .  137 ?   14.970  26.942  16.300  0.00  0   A
-ATOM     1014    C    C .  LEU   A .  137 ?   16.652  27.030  14.689  0.00  0   A
-ATOM     1015    O    O .  LEU   A .  137 ?   16.968  28.209  14.932  0.00  0   A
-ATOM     1280    C  CD2 .  PHE   A .  174 ?   15.409  30.643  25.623  0.00  0   A
-ATOM     1287    O    O .  PRO   A .  175 ?   19.472  32.424  20.666  0.00  0   A
-ATOM     1289    C   CG .  PRO   A .  175 ?   18.737  29.443  21.033  0.00  0   A
-ATOM     1290    C   CD .  PRO   A .  175 ?   18.295  29.738  22.438  0.00  0   A
-ATOM     1309    C   CA .  TRP   A .  178 ?   18.854  33.025  17.137  0.00  0   A
-ATOM     1310    C    C .  TRP   A .  178 ?   17.481  33.558  17.564  0.00  0   A
-ATOM     1311    O    O .  TRP   A .  178 ?   16.495  33.261  16.896 -2.14  0   A
-ATOM     1312    C   CB .  TRP   A .  178 ?   18.807  31.481  17.128  0.00  0   A
-ATOM     1322    N    N .  THR   A .  179 ?   17.421  34.347  18.657  0.00  0   A
-ATOM     1323    C   CA .  THR   A .  179 ?   16.193  34.623  19.411  0.00  0   A
-ATOM     1324    C    C .  THR   A .  179 ?   15.545  35.958  19.044  0.00  0   A
-ATOM     1326    C   CB .  THR   A .  179 ?   16.508  34.581  20.893  0.00  0   A
-ATOM     1327    O  OG1 .  THR   A .  179 ?   17.108  33.330  21.134 -2.14  0   A
-ATOM     1328    C  CG2 .  THR   A .  179 ?   15.235  34.657  21.794  0.00  0   A
-ATOM     1329    N    N .  ALA   A .  180 ?   14.229  35.929  18.757 -1.09  0   A
-ATOM     1333    C   CB .  ALA   A .  180 ?   12.155  36.812  17.751  0.00  0   A
-ATOM     1354    C   CB .  SER   A .  183 ?   11.829  35.508  22.060  0.00  0   A
-ATOM     1355    O   OG .  SER   A .  183 ?   10.954  35.267  20.964  0.00  0   A
-ATOM     1405    C  CD2 .  PHE   A .  189 ?   10.703  31.452  22.157  0.00  0   A
-ATOM     1407    C  CE2 .  PHE   A .  189 ?   11.966  31.656  22.739  0.00  0   A
-ATOM     1408    C   CZ .  PHE   A .  189 ?   12.053  32.229  24.016  0.00  0   A
-ATOM     1433    C   CA .  SER   A .  193 ?    9.893  34.090  16.472  0.00  0   A
-ATOM     1434    C    C .  SER   A .  193 ?   10.658  32.899  15.802  0.00  0   A
-ATOM     1435    O    O .  SER   A .  193 ?   11.879  32.960  15.552 -3.21  0   A
-ATOM     1436    C   CB .  SER   A .  193 ?    9.997  34.149  17.982  0.00  0   A
-ATOM     1437    O   OG .  SER   A .  193 ?    9.317  33.077  18.605  0.00  0   A
-ATOM     1438    N    N .  ASP   A .  194 ?    9.907  31.853  15.450  0.00  0   A
-ATOM     1439    C   CA .  ASP   A .  194 ?   10.435  30.800  14.622  0.00  0   A
-ATOM     1444    O  OD1 .  ASP   A .  194 ?   10.115  28.834  16.531  0.00  0   A
-ATOM     1471    C   CB .  ALA   A .  197 ?   14.926  31.065  14.885  0.00  0   A
+ATOM    993      N    N ?  ARG    Axp 135 ?   10.598   26.723   18.417   0.00  0 362 A
+ATOM    994      C   CA ?  ARG    Axp 135 ?   11.309   27.407   19.509   0.00  0 362 A
+ATOM    995      C    C ?  ARG    Axp 135 ?   12.856   27.406   19.519   0.00  0 362 A
+ATOM    996      O    O ?  ARG    Axp 135 ?   13.454   28.096   20.320  -4.69  0 362 A
+ATOM    997      C   CB ?  ARG    Axp 135 ?   10.850   26.919   20.881   0.00  0 362 A
+ATOM    1004     N    N ?  ASP    Axp 136 ?   13.515   26.641   18.666   0.00  0 363 A
+ATOM    1005     C   CA ?  ASP    Axp 136 ?   14.988   26.627   18.681   0.00  0 363 A
+ATOM    1006     C    C ?  ASP    Axp 136 ?   15.413   26.185   17.291   0.00  0 363 A
+ATOM    1008     C   CB ?  ASP    Axp 136 ?   15.490   25.673   19.755   0.00  0 363 A
+ATOM    1009     C   CG ?  ASP    Axp 136 ?   16.996   25.759   19.996   0.00  0 363 A
+ATOM    1010     O  OD1 ?  ASP    Axp 136 ?   17.712   26.739   19.639   0.00  0 363 A
+ATOM    1012     N    N ?  LEU    Axp 137 ?   14.970   26.942   16.300   0.00  0 364 A
+ATOM    1014     C    C ?  LEU    Axp 137 ?   16.652   27.030   14.689   0.00  0 364 A
+ATOM    1015     O    O ?  LEU    Axp 137 ?   16.968   28.209   14.932   0.00  0 364 A
+ATOM    1280     C  CD2 ?  PHE    Axp 174 ?   15.409   30.643   25.623   0.00  0 401 A
+ATOM    1287     O    O ?  PRO    Axp 175 ?   19.472   32.424   20.666   0.00  0 402 A
+ATOM    1289     C   CG ?  PRO    Axp 175 ?   18.737   29.443   21.033   0.00  0 402 A
+ATOM    1290     C   CD ?  PRO    Axp 175 ?   18.295   29.738   22.438   0.00  0 402 A
+ATOM    1309     C   CA ?  TRP    Axp 178 ?   18.854   33.025   17.137   0.00  0 405 A
+ATOM    1310     C    C ?  TRP    Axp 178 ?   17.481   33.558   17.564   0.00  0 405 A
+ATOM    1311     O    O ?  TRP    Axp 178 ?   16.495   33.261   16.896  -2.14  0 405 A
+ATOM    1312     C   CB ?  TRP    Axp 178 ?   18.807   31.481   17.128   0.00  0 405 A
+ATOM    1322     N    N ?  THR    Axp 179 ?   17.421   34.347   18.657   0.00  0 406 A
+ATOM    1323     C   CA ?  THR    Axp 179 ?   16.193   34.623   19.411   0.00  0 406 A
+ATOM    1324     C    C ?  THR    Axp 179 ?   15.545   35.958   19.044   0.00  0 406 A
+ATOM    1326     C   CB ?  THR    Axp 179 ?   16.508   34.581   20.893   0.00  0 406 A
+ATOM    1327     O  OG1 ?  THR    Axp 179 ?   17.108   33.330   21.134  -2.14  0 406 A
+ATOM    1328     C  CG2 ?  THR    Axp 179 ?   15.235   34.657   21.794   0.00  0 406 A
+ATOM    1329     N    N ?  ALA    Axp 180 ?   14.229   35.929   18.757  -1.09  0 407 A
+ATOM    1333     C   CB ?  ALA    Axp 180 ?   12.155   36.812   17.751   0.00  0 407 A
+ATOM    1354     C   CB ?  SER    Axp 183 ?   11.829   35.508   22.060   0.00  0 410 A
+ATOM    1355     O   OG ?  SER    Axp 183 ?   10.954   35.267   20.964   0.00  0 410 A
+ATOM    1405     C  CD2 ?  PHE    Axp 189 ?   10.703   31.452   22.157   0.00  0 416 A
+ATOM    1407     C  CE2 ?  PHE    Axp 189 ?   11.966   31.656   22.739   0.00  0 416 A
+ATOM    1408     C   CZ ?  PHE    Axp 189 ?   12.053   32.229   24.016   0.00  0 416 A
+ATOM    1433     C   CA ?  SER    Axp 193 ?    9.893   34.090   16.472   0.00  0 420 A
+ATOM    1434     C    C ?  SER    Axp 193 ?   10.658   32.899   15.802   0.00  0 420 A
+ATOM    1435     O    O ?  SER    Axp 193 ?   11.879   32.960   15.552  -3.21  0 420 A
+ATOM    1436     C   CB ?  SER    Axp 193 ?    9.997   34.149   17.982   0.00  0 420 A
+ATOM    1437     O   OG ?  SER    Axp 193 ?    9.317   33.077   18.605   0.00  0 420 A
+ATOM    1438     N    N ?  ASP    Axp 194 ?    9.907   31.853   15.450   0.00  0 421 A
+ATOM    1439     C   CA ?  ASP    Axp 194 ?   10.435   30.800   14.622   0.00  0 421 A
+ATOM    1444     O  OD1 ?  ASP    Axp 194 ?   10.115   28.834   16.531   0.00  0 421 A
+ATOM    1471     C   CB ?  ALA    Axp 197 ?   14.926   31.065   14.885   0.00  0 424 A
 #
--- a/tests/reference_output/123abc_out/pocket12_atm.cif
+++ b/tests/reference_output/123abc_out/pocket12_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    12:
 6  - Hydrophobicity Score              : 14.1667
 7  - Polarity Score                    :     7
 8  - Amino Acid based volume Score     : 4.4167
-9  - Pocket volume (Monte Carlo)       : 292.3979
+9  - Pocket volume (Monte Carlo)       : 288.4808
 10  -Pocket volume (convex hull)       : 19.5893
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 1.0000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,24 +37,25 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
-ATOM     3271    O   OG .  SER   B .  158 ?   19.353  51.914  34.201 -4.02  0   B
-ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
-ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
-ATOM     3383    C  CE2 .  PHE   B .  174 ?   15.221  45.900  34.664  0.00  0   B
-ATOM     3094    O    O .  ARG   B .  135 ?   14.784  48.309  40.445 -7.50  0   B
-ATOM     3097    C   CD .  ARG   B .  135 ?   10.822  49.558  37.921  0.00  0   B
-ATOM     3504    C  CE2 .  PHE   B .  189 ?   12.691  45.021  38.263  0.00  0   B
-ATOM     3368    O    O .  LYS   B .  173 ?   18.932  47.542  34.352 -3.62  0   B
-ATOM     3109    O  OD2 .  ASP   B .  136 ?   19.063  51.084  39.753 -0.40  0   B
-ATOM     3258    N    N .  LEU   B .  157 ?   20.869  54.873  37.697  0.00  0   B
-ATOM     3095    C   CB .  ARG   B .  135 ?   12.276  49.729  39.764  0.00  0   B
-ATOM     3084    O    O .  HIS   B .  134 ?   12.372  52.048  41.332 -1.07  0   B
-ATOM     3381    C  CD2 .  PHE   B .  174 ?   16.430  45.506  35.243  0.00  0   B
-ATOM     3270    C   CB .  SER   B .  158 ?   20.116  50.947  34.907  0.00  0   B
-ATOM     3326    C  CE2 .  TYR   B .  166 ?   21.152  49.314  38.053  0.00  0   B
-ATOM     3391    C   CD .  PRO   B .  175 ?   19.172  45.854  38.445  0.00  0   B
-ATOM     3106    C   CB .  ASP   B .  136 ?   17.005  50.806  40.933  0.00  0   B
-ATOM     3107    C   CG .  ASP   B .  136 ?   18.465  50.434  40.626  0.00  0   B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3271     O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3383     C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM    3094     O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM    3097     C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM    3504     C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM    3368     O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM    3109     O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM    3258     N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM    3095     C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM    3084     O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM    3381     C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM    3270     C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM    3326     C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM    3391     C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM    3106     C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM    3107     C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
 # 
--- a/tests/reference_output/123abc_out/pocket12_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket12_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,43 +15,44 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3084    O    O .  HIS   B .  134 ?   12.372  52.048  41.332 -1.07  0   B
-ATOM     3092    C   CA .  ARG   B .  135 ?   12.705  49.230  41.141  0.00  0   B
-ATOM     3093    C    C .  ARG   B .  135 ?   14.235  49.115  41.170  0.00  0   B
-ATOM     3094    O    O .  ARG   B .  135 ?   14.784  48.309  40.445 -7.50  0   B
-ATOM     3095    C   CB .  ARG   B .  135 ?   12.276  49.729  39.764  0.00  0   B
-ATOM     3096    C   CG .  ARG   B .  135 ?   10.987  49.132  39.313  0.00  0   B
-ATOM     3097    C   CD .  ARG   B .  135 ?   10.822  49.558  37.921  0.00  0   B
-ATOM     3098    N   NE .  ARG   B .  135 ?    9.837  48.697  37.316 -3.28  0   B
-ATOM     3099    C   CZ .  ARG   B .  135 ?    9.680  48.564  36.008  0.00  0   B
-ATOM     3100    N  NH1 .  ARG   B .  135 ?   10.479  49.242  35.166  0.00  0   B
-ATOM     3102    N    N .  ASP   B .  136 ?   14.929  49.943  41.933  0.00  0   B
-ATOM     3103    C   CA .  ASP   B .  136 ?   16.383  49.878  41.974  0.00  0   B
-ATOM     3106    C   CB .  ASP   B .  136 ?   17.005  50.806  40.933  0.00  0   B
-ATOM     3107    C   CG .  ASP   B .  136 ?   18.465  50.434  40.626  0.00  0   B
-ATOM     3108    O  OD1 .  ASP   B .  136 ?   19.011  49.469  41.230 -2.14  0   B
-ATOM     3109    O  OD2 .  ASP   B .  136 ?   19.063  51.084  39.753 -0.40  0   B
-ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
-ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
-ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
-ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
-ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
-ATOM     3256    C    C .  GLY   B .  156 ?   20.360  55.778  36.866  0.00  0   B
-ATOM     3258    N    N .  LEU   B .  157 ?   20.869  54.873  37.697  0.00  0   B
-ATOM     3266    N    N .  SER   B .  158 ?   21.413  52.688  36.129  0.00  0   B
-ATOM     3267    C   CA .  SER   B .  158 ?   21.516  51.514  35.236  0.00  0   B
-ATOM     3270    C   CB .  SER   B .  158 ?   20.116  50.947  34.907  0.00  0   B
-ATOM     3271    O   OG .  SER   B .  158 ?   19.353  51.914  34.201 -4.02  0   B
-ATOM     3324    C  CD2 .  TYR   B .  166 ?   21.644  48.614  37.025  0.00  0   B
-ATOM     3326    C  CE2 .  TYR   B .  166 ?   21.152  49.314  38.053  0.00  0   B
-ATOM     3368    O    O .  LYS   B .  173 ?   18.932  47.542  34.352 -3.62  0   B
-ATOM     3375    C   CA .  PHE   B .  174 ?   19.360  45.109  35.564  0.00  0   B
-ATOM     3381    C  CD2 .  PHE   B .  174 ?   16.430  45.506  35.243  0.00  0   B
-ATOM     3383    C  CE2 .  PHE   B .  174 ?   15.221  45.900  34.664  0.00  0   B
-ATOM     3390    C   CG .  PRO   B .  175 ?   19.698  46.334  39.774  0.00  0   B
-ATOM     3391    C   CD .  PRO   B .  175 ?   19.172  45.854  38.445  0.00  0   B
-ATOM     3502    C  CD2 .  PHE   B .  189 ?   11.410  45.318  38.790  0.00  0   B
-ATOM     3504    C  CE2 .  PHE   B .  189 ?   12.691  45.021  38.263  0.00  0   B
-ATOM     3505    C   CZ .  PHE   B .  189 ?   12.791  44.477  36.970  0.00  0   B
+ATOM    3084     O    O ?  HIS    Bxp 134 ?   12.372   52.048   41.332  -1.07  0 361 B
+ATOM    3092     C   CA ?  ARG    Bxp 135 ?   12.705   49.230   41.141   0.00  0 362 B
+ATOM    3093     C    C ?  ARG    Bxp 135 ?   14.235   49.115   41.170   0.00  0 362 B
+ATOM    3094     O    O ?  ARG    Bxp 135 ?   14.784   48.309   40.445  -7.50  0 362 B
+ATOM    3095     C   CB ?  ARG    Bxp 135 ?   12.276   49.729   39.764   0.00  0 362 B
+ATOM    3096     C   CG ?  ARG    Bxp 135 ?   10.987   49.132   39.313   0.00  0 362 B
+ATOM    3097     C   CD ?  ARG    Bxp 135 ?   10.822   49.558   37.921   0.00  0 362 B
+ATOM    3098     N   NE ?  ARG    Bxp 135 ?    9.837   48.697   37.316  -3.28  0 362 B
+ATOM    3099     C   CZ ?  ARG    Bxp 135 ?    9.680   48.564   36.008   0.00  0 362 B
+ATOM    3100     N  NH1 ?  ARG    Bxp 135 ?   10.479   49.242   35.166   0.00  0 362 B
+ATOM    3102     N    N ?  ASP    Bxp 136 ?   14.929   49.943   41.933   0.00  0 363 B
+ATOM    3103     C   CA ?  ASP    Bxp 136 ?   16.383   49.878   41.974   0.00  0 363 B
+ATOM    3106     C   CB ?  ASP    Bxp 136 ?   17.005   50.806   40.933   0.00  0 363 B
+ATOM    3107     C   CG ?  ASP    Bxp 136 ?   18.465   50.434   40.626   0.00  0 363 B
+ATOM    3108     O  OD1 ?  ASP    Bxp 136 ?   19.011   49.469   41.230  -2.14  0 363 B
+ATOM    3109     O  OD2 ?  ASP    Bxp 136 ?   19.063   51.084   39.753  -0.40  0 363 B
+ATOM    3240     C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3254     N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3256     C    C ?  GLY    Bxp 156 ?   20.360   55.778   36.866   0.00  0 383 B
+ATOM    3258     N    N ?  LEU    Bxp 157 ?   20.869   54.873   37.697   0.00  0 384 B
+ATOM    3266     N    N ?  SER    Bxp 158 ?   21.413   52.688   36.129   0.00  0 385 B
+ATOM    3267     C   CA ?  SER    Bxp 158 ?   21.516   51.514   35.236   0.00  0 385 B
+ATOM    3270     C   CB ?  SER    Bxp 158 ?   20.116   50.947   34.907   0.00  0 385 B
+ATOM    3271     O   OG ?  SER    Bxp 158 ?   19.353   51.914   34.201  -4.02  0 385 B
+ATOM    3324     C  CD2 ?  TYR    Bxp 166 ?   21.644   48.614   37.025   0.00  0 393 B
+ATOM    3326     C  CE2 ?  TYR    Bxp 166 ?   21.152   49.314   38.053   0.00  0 393 B
+ATOM    3368     O    O ?  LYS    Bxp 173 ?   18.932   47.542   34.352  -3.62  0 400 B
+ATOM    3375     C   CA ?  PHE    Bxp 174 ?   19.360   45.109   35.564   0.00  0 401 B
+ATOM    3381     C  CD2 ?  PHE    Bxp 174 ?   16.430   45.506   35.243   0.00  0 401 B
+ATOM    3383     C  CE2 ?  PHE    Bxp 174 ?   15.221   45.900   34.664   0.00  0 401 B
+ATOM    3390     C   CG ?  PRO    Bxp 175 ?   19.698   46.334   39.774   0.00  0 402 B
+ATOM    3391     C   CD ?  PRO    Bxp 175 ?   19.172   45.854   38.445   0.00  0 402 B
+ATOM    3502     C  CD2 ?  PHE    Bxp 189 ?   11.410   45.318   38.790   0.00  0 416 B
+ATOM    3504     C  CE2 ?  PHE    Bxp 189 ?   12.691   45.021   38.263   0.00  0 416 B
+ATOM    3505     C   CZ ?  PHE    Bxp 189 ?   12.791   44.477   36.970   0.00  0 416 B
 #
--- a/tests/reference_output/123abc_out/pocket13_atm.cif
+++ b/tests/reference_output/123abc_out/pocket13_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    13:
 6  - Hydrophobicity Score              : 59.0769
 7  - Polarity Score                    :     0
 8  - Amino Acid based volume Score     : 3.6154
-9  - Pocket volume (Monte Carlo)       : 403.2792
+9  - Pocket volume (Monte Carlo)       : 411.4784
 10  -Pocket volume (convex hull)       : 39.2787
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 37.1163
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,37 +37,38 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     7064    N    N .  VAL   D .  111 ?   48.340  24.744  22.841  0.00  0   D
-ATOM     7069    C  CG1 .  VAL   D .  111 ?   50.065  24.177  20.697  0.00  0   D
-ATOM     7068    C   CB .  VAL   D .  111 ?   49.531  23.019  21.320  0.00  0   D
-ATOM     7063    C   CB .  ALA   D .  110 ?   45.905  26.806  22.761  0.00  0   D
-ATOM     8096    C  CG1 .  VAL   D .  241 ?   40.339  21.749  29.386  0.00  0   D
-ATOM     7780    O    O .  LEU   D .  202 ?   42.550  24.062  33.744  0.00  0   D
-ATOM     7784    C  CD2 .  LEU   D .  202 ?   42.820  19.922  32.429  0.00  0   D
-ATOM     7814    C  CG2 .  ILE   D .  205 ?   46.612  24.182  31.921  0.00  0   D
-ATOM     7081    O    O .  LEU   D .  113 ?   47.597  21.725  29.219 -1.07  0   D
-ATOM     7086    N    N .  LEU   D .  114 ?   47.359  21.989  26.988  0.00  0   D
-ATOM     7087    C   CA .  LEU   D .  114 ?   46.823  20.670  26.737  0.00  0   D
-ATOM     7080    C    C .  LEU   D .  113 ?   47.767  22.386  28.183  0.00  0   D
-ATOM     7062    O    O .  ALA   D .  110 ?   47.080  24.204  24.629 -3.21  0   D
-ATOM     7093    C  CD2 .  LEU   D .  114 ?   45.275  20.097  23.190  0.00  0   D
-ATOM     8079    C   CG .  PRO   D .  238 ?   40.497  24.257  24.472  0.00  0   D
-ATOM     7061    C    C .  ALA   D .  110 ?   47.472  25.051  23.811  0.00  0   D
-ATOM     8080    C   CD .  PRO   D .  238 ?   40.408  25.135  25.676  0.00  0   D
-ATOM     8067    O    O .  GLY   D .  236 ?   40.728  28.470  25.473 -1.21  0   D
-ATOM     7060    C   CA .  ALA   D .  110 ?   46.959  26.484  23.905  0.00  0   D
-ATOM     7084    C  CD1 .  LEU   D .  113 ?   46.418  27.158  28.740  0.00  0   D
-ATOM     7817    C   CA .  ALA   D .  206 ?   43.249  27.236  31.702  0.00  0   D
-ATOM     7819    O    O .  ALA   D .  206 ?   43.166  29.530  31.087 -4.69  0   D
-ATOM     8069    C   CA .  CYS   D .  237 ?   39.173  27.291  27.413  0.00  0   D
-ATOM     7118    C   CB .  ALA   D .  117 ?   45.712  18.926  30.827  0.00  0   D
-ATOM     7820    C   CB .  ALA   D .  206 ?   41.725  26.810  31.590  0.00  0   D
-ATOM     8073    S   SG .  CYS   D .  237 ?   38.662  25.215  29.286  0.00  0   D
-ATOM     7816    N    N .  ALA   D .  206 ?   43.950  26.440  32.723  0.00  0   D
-ATOM     7065    C   CA .  VAL   D .  111 ?   48.863  23.360  22.717  0.00  0   D
-ATOM     7082    C   CB .  LEU   D .  113 ?   47.325  24.825  28.299  0.00  0   D
-ATOM     8097    C  CG2 .  VAL   D .  241 ?   40.590  21.066  26.854  0.00  0   D
-ATOM     7092    C  CD1 .  LEU   D .  114 ?   44.050  19.857  25.449  0.00  0   D
-ATOM     8308    C  CE1 .  PHE   D .  266 ?   42.431  17.800  28.875  0.00  0   D
+ATOM    7064     N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM    7069     C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM    7068     C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM    7063     C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM    8096     C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM    7780     O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM    7784     C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM    7814     C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM    7081     O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM    7086     N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM    7087     C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM    7080     C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM    7062     O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM    7093     C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM    8079     C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM    7061     C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM    8080     C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM    8067     O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM    7060     C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM    7084     C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM    7817     C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM    7819     O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM    8069     C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM    7118     C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM    7820     C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM    8073     S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM    7816     N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM    7065     C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM    7082     C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM    8097     C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM    7092     C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM    8308     C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
 # 
--- a/tests/reference_output/123abc_out/pocket13_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket13_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,55 +15,56 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     7059    N    N .  ALA   D .  110 ?   48.007  27.461  23.893 -1.09  0   D
-ATOM     7060    C   CA .  ALA   D .  110 ?   46.959  26.484  23.905  0.00  0   D
-ATOM     7061    C    C .  ALA   D .  110 ?   47.472  25.051  23.811  0.00  0   D
-ATOM     7062    O    O .  ALA   D .  110 ?   47.080  24.204  24.629 -3.21  0   D
-ATOM     7063    C   CB .  ALA   D .  110 ?   45.905  26.806  22.761  0.00  0   D
-ATOM     7064    N    N .  VAL   D .  111 ?   48.340  24.744  22.841  0.00  0   D
-ATOM     7065    C   CA .  VAL   D .  111 ?   48.863  23.360  22.717  0.00  0   D
-ATOM     7068    C   CB .  VAL   D .  111 ?   49.531  23.019  21.320  0.00  0   D
-ATOM     7069    C  CG1 .  VAL   D .  111 ?   50.065  24.177  20.697  0.00  0   D
-ATOM     7079    C   CA .  LEU   D .  113 ?   48.430  23.739  28.221  0.00  0   D
-ATOM     7080    C    C .  LEU   D .  113 ?   47.767  22.386  28.183  0.00  0   D
-ATOM     7081    O    O .  LEU   D .  113 ?   47.597  21.725  29.219 -1.07  0   D
-ATOM     7082    C   CB .  LEU   D .  113 ?   47.325  24.825  28.299  0.00  0   D
-ATOM     7083    C   CG .  LEU   D .  113 ?   47.664  26.335  28.429  0.00  0   D
-ATOM     7084    C  CD1 .  LEU   D .  113 ?   46.418  27.158  28.740  0.00  0   D
-ATOM     7086    N    N .  LEU   D .  114 ?   47.359  21.989  26.988  0.00  0   D
-ATOM     7087    C   CA .  LEU   D .  114 ?   46.823  20.670  26.737  0.00  0   D
-ATOM     7090    C   CB .  LEU   D .  114 ?   46.375  20.660  25.286  0.00  0   D
-ATOM     7091    C   CG .  LEU   D .  114 ?   45.386  19.662  24.699  0.00  0   D
-ATOM     7092    C  CD1 .  LEU   D .  114 ?   44.050  19.857  25.449  0.00  0   D
-ATOM     7093    C  CD2 .  LEU   D .  114 ?   45.275  20.097  23.190  0.00  0   D
-ATOM     7118    C   CB .  ALA   D .  117 ?   45.712  18.926  30.827  0.00  0   D
-ATOM     7778    C   CA .  LEU   D .  202 ?   42.652  21.867  34.762  0.00  0   D
-ATOM     7779    C    C .  LEU   D .  202 ?   42.175  23.314  34.680  0.00  0   D
-ATOM     7780    O    O .  LEU   D .  202 ?   42.550  24.062  33.744  0.00  0   D
-ATOM     7781    C   CB .  LEU   D .  202 ?   41.521  21.052  34.137  0.00  0   D
-ATOM     7784    C  CD2 .  LEU   D .  202 ?   42.820  19.922  32.429  0.00  0   D
-ATOM     7810    C    C .  ILE   D .  205 ?   45.268  26.571  32.956  0.00  0   D
-ATOM     7812    C   CB .  ILE   D .  205 ?   46.098  24.078  33.335  0.00  0   D
-ATOM     7814    C  CG2 .  ILE   D .  205 ?   46.612  24.182  31.921  0.00  0   D
-ATOM     7816    N    N .  ALA   D .  206 ?   43.950  26.440  32.723  0.00  0   D
-ATOM     7817    C   CA .  ALA   D .  206 ?   43.249  27.236  31.702  0.00  0   D
-ATOM     7818    C    C .  ALA   D .  206 ?   43.351  28.736  31.982  0.00  0   D
-ATOM     7819    O    O .  ALA   D .  206 ?   43.166  29.530  31.087 -4.69  0   D
-ATOM     7820    C   CB .  ALA   D .  206 ?   41.725  26.810  31.590  0.00  0   D
-ATOM     8066    C    C .  GLY   D .  236 ?   39.903  29.189  26.105  0.00  0   D
-ATOM     8067    O    O .  GLY   D .  236 ?   40.728  28.470  25.473 -1.21  0   D
-ATOM     8068    N    N .  CYS   D .  237 ?   39.113  28.714  27.084  0.00  0   D
-ATOM     8069    C   CA .  CYS   D .  237 ?   39.173  27.291  27.413  0.00  0   D
-ATOM     8072    C   CB .  CYS   D .  237 ?   38.727  27.002  28.857  0.00  0   D
-ATOM     8073    S   SG .  CYS   D .  237 ?   38.662  25.215  29.286  0.00  0   D
-ATOM     8074    N    N .  PRO   D .  238 ?   38.989  25.529  25.691  0.00  0   D
-ATOM     8079    C   CG .  PRO   D .  238 ?   40.497  24.257  24.472  0.00  0   D
-ATOM     8080    C   CD .  PRO   D .  238 ?   40.408  25.135  25.676  0.00  0   D
-ATOM     8095    C   CB .  VAL   D .  241 ?   39.605  21.580  27.947  0.00  0   D
-ATOM     8096    C  CG1 .  VAL   D .  241 ?   40.339  21.749  29.386  0.00  0   D
-ATOM     8097    C  CG2 .  VAL   D .  241 ?   40.590  21.066  26.854  0.00  0   D
-ATOM     8306    C  CD1 .  PHE   D .  266 ?   43.156  16.946  28.042  0.00  0   D
-ATOM     8308    C  CE1 .  PHE   D .  266 ?   42.431  17.800  28.875  0.00  0   D
-ATOM     8310    C   CZ .  PHE   D .  266 ?   42.081  17.395  30.126  0.00  0   D
+ATOM    7059     N    N ?  ALA    Dxp 110 ?   48.007   27.461   23.893  -1.09  0 337 D
+ATOM    7060     C   CA ?  ALA    Dxp 110 ?   46.959   26.484   23.905   0.00  0 337 D
+ATOM    7061     C    C ?  ALA    Dxp 110 ?   47.472   25.051   23.811   0.00  0 337 D
+ATOM    7062     O    O ?  ALA    Dxp 110 ?   47.080   24.204   24.629  -3.21  0 337 D
+ATOM    7063     C   CB ?  ALA    Dxp 110 ?   45.905   26.806   22.761   0.00  0 337 D
+ATOM    7064     N    N ?  VAL    Dxp 111 ?   48.340   24.744   22.841   0.00  0 338 D
+ATOM    7065     C   CA ?  VAL    Dxp 111 ?   48.863   23.360   22.717   0.00  0 338 D
+ATOM    7068     C   CB ?  VAL    Dxp 111 ?   49.531   23.019   21.320   0.00  0 338 D
+ATOM    7069     C  CG1 ?  VAL    Dxp 111 ?   50.065   24.177   20.697   0.00  0 338 D
+ATOM    7079     C   CA ?  LEU    Dxp 113 ?   48.430   23.739   28.221   0.00  0 340 D
+ATOM    7080     C    C ?  LEU    Dxp 113 ?   47.767   22.386   28.183   0.00  0 340 D
+ATOM    7081     O    O ?  LEU    Dxp 113 ?   47.597   21.725   29.219  -1.07  0 340 D
+ATOM    7082     C   CB ?  LEU    Dxp 113 ?   47.325   24.825   28.299   0.00  0 340 D
+ATOM    7083     C   CG ?  LEU    Dxp 113 ?   47.664   26.335   28.429   0.00  0 340 D
+ATOM    7084     C  CD1 ?  LEU    Dxp 113 ?   46.418   27.158   28.740   0.00  0 340 D
+ATOM    7086     N    N ?  LEU    Dxp 114 ?   47.359   21.989   26.988   0.00  0 341 D
+ATOM    7087     C   CA ?  LEU    Dxp 114 ?   46.823   20.670   26.737   0.00  0 341 D
+ATOM    7090     C   CB ?  LEU    Dxp 114 ?   46.375   20.660   25.286   0.00  0 341 D
+ATOM    7091     C   CG ?  LEU    Dxp 114 ?   45.386   19.662   24.699   0.00  0 341 D
+ATOM    7092     C  CD1 ?  LEU    Dxp 114 ?   44.050   19.857   25.449   0.00  0 341 D
+ATOM    7093     C  CD2 ?  LEU    Dxp 114 ?   45.275   20.097   23.190   0.00  0 341 D
+ATOM    7118     C   CB ?  ALA    Dxp 117 ?   45.712   18.926   30.827   0.00  0 344 D
+ATOM    7778     C   CA ?  LEU    Dxp 202 ?   42.652   21.867   34.762   0.00  0 429 D
+ATOM    7779     C    C ?  LEU    Dxp 202 ?   42.175   23.314   34.680   0.00  0 429 D
+ATOM    7780     O    O ?  LEU    Dxp 202 ?   42.550   24.062   33.744   0.00  0 429 D
+ATOM    7781     C   CB ?  LEU    Dxp 202 ?   41.521   21.052   34.137   0.00  0 429 D
+ATOM    7784     C  CD2 ?  LEU    Dxp 202 ?   42.820   19.922   32.429   0.00  0 429 D
+ATOM    7810     C    C ?  ILE    Dxp 205 ?   45.268   26.571   32.956   0.00  0 432 D
+ATOM    7812     C   CB ?  ILE    Dxp 205 ?   46.098   24.078   33.335   0.00  0 432 D
+ATOM    7814     C  CG2 ?  ILE    Dxp 205 ?   46.612   24.182   31.921   0.00  0 432 D
+ATOM    7816     N    N ?  ALA    Dxp 206 ?   43.950   26.440   32.723   0.00  0 433 D
+ATOM    7817     C   CA ?  ALA    Dxp 206 ?   43.249   27.236   31.702   0.00  0 433 D
+ATOM    7818     C    C ?  ALA    Dxp 206 ?   43.351   28.736   31.982   0.00  0 433 D
+ATOM    7819     O    O ?  ALA    Dxp 206 ?   43.166   29.530   31.087  -4.69  0 433 D
+ATOM    7820     C   CB ?  ALA    Dxp 206 ?   41.725   26.810   31.590   0.00  0 433 D
+ATOM    8066     C    C ?  GLY    Dxp 236 ?   39.903   29.189   26.105   0.00  0 463 D
+ATOM    8067     O    O ?  GLY    Dxp 236 ?   40.728   28.470   25.473  -1.21  0 463 D
+ATOM    8068     N    N ?  CYS    Dxp 237 ?   39.113   28.714   27.084   0.00  0 464 D
+ATOM    8069     C   CA ?  CYS    Dxp 237 ?   39.173   27.291   27.413   0.00  0 464 D
+ATOM    8072     C   CB ?  CYS    Dxp 237 ?   38.727   27.002   28.857   0.00  0 464 D
+ATOM    8073     S   SG ?  CYS    Dxp 237 ?   38.662   25.215   29.286   0.00  0 464 D
+ATOM    8074     N    N ?  PRO    Dxp 238 ?   38.989   25.529   25.691   0.00  0 465 D
+ATOM    8079     C   CG ?  PRO    Dxp 238 ?   40.497   24.257   24.472   0.00  0 465 D
+ATOM    8080     C   CD ?  PRO    Dxp 238 ?   40.408   25.135   25.676   0.00  0 465 D
+ATOM    8095     C   CB ?  VAL    Dxp 241 ?   39.605   21.580   27.947   0.00  0 468 D
+ATOM    8096     C  CG1 ?  VAL    Dxp 241 ?   40.339   21.749   29.386   0.00  0 468 D
+ATOM    8097     C  CG2 ?  VAL    Dxp 241 ?   40.590   21.066   26.854   0.00  0 468 D
+ATOM    8306     C  CD1 ?  PHE    Dxp 266 ?   43.156   16.946   28.042   0.00  0 493 D
+ATOM    8308     C  CE1 ?  PHE    Dxp 266 ?   42.431   17.800   28.875   0.00  0 493 D
+ATOM    8310     C   CZ ?  PHE    Dxp 266 ?   42.081   17.395   30.126   0.00  0 493 D
 #
--- a/tests/reference_output/123abc_out/pocket14_atm.cif
+++ b/tests/reference_output/123abc_out/pocket14_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    14:
 6  - Hydrophobicity Score              : -27.2500
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 3.5000
-9  - Pocket volume (Monte Carlo)       : 155.2399
+9  - Pocket volume (Monte Carlo)       : 158.8699
 10  -Pocket volume (convex hull)       : 1.4197
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 0.0000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,18 +37,19 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3238    O    O .  ASP   B .  154 ?   17.212  58.730  41.018 -2.14  0   B
-ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
-ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
-ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
-ATOM     2491    O  OE1 .  GLU   B .   59 ?   14.831  61.607  36.581  0.00  0   B
-ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
-ATOM     2492    O  OE2 .  GLU   B .   59 ?   15.137  61.777  38.754 -1.07  0   B
-ATOM     2389    N   NZ .  LYS   B .   44 ?   17.801  61.554  36.438 -1.51  0   B
-ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
-ATOM     2489    C   CG .  GLU   B .   59 ?   12.912  61.584  38.000  0.00  0   B
-ATOM     2490    C   CD .  GLU   B .   59 ?   14.404  61.663  37.759  0.00  0   B
-ATOM     3239    C   CB .  ASP   B .  154 ?   15.520  56.620  41.941  0.00  0   B
-ATOM     2488    C   CB .  GLU   B .   59 ?   12.087  61.638  36.697  0.00  0   B
+ATOM    3238     O    O ?  ASP    Bxp 154 ?   17.212   58.730   41.018  -2.14  0 381 B
+ATOM    3240     C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    2491     O  OE1 ?  GLU    Bxp 59 ?   14.831   61.607   36.581   0.00  0 286 B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    2492     O  OE2 ?  GLU    Bxp 59 ?   15.137   61.777   38.754  -1.07  0 286 B
+ATOM    2389     N   NZ ?  LYS    Bxp 44 ?   17.801   61.554   36.438  -1.51  0 271 B
+ATOM    3254     N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM    2489     C   CG ?  GLU    Bxp 59 ?   12.912   61.584   38.000   0.00  0 286 B
+ATOM    2490     C   CD ?  GLU    Bxp 59 ?   14.404   61.663   37.759   0.00  0 286 B
+ATOM    3239     C   CB ?  ASP    Bxp 154 ?   15.520   56.620   41.941   0.00  0 381 B
+ATOM    2488     C   CB ?  GLU    Bxp 59 ?   12.087   61.638   36.697   0.00  0 286 B
 # 
--- a/tests/reference_output/123abc_out/pocket14_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket14_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,23 +15,24 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     2389    N   NZ .  LYS   B .   44 ?   17.801  61.554  36.438 -1.51  0   B
-ATOM     2454    O    O .  GLU   B .   55 ?   11.608  61.345  33.284 -1.88  0   B
-ATOM     2485    C   CA .  GLU   B .   59 ?   10.598  61.833  36.936  0.00  0   B
-ATOM     2488    C   CB .  GLU   B .   59 ?   12.087  61.638  36.697  0.00  0   B
-ATOM     2489    C   CG .  GLU   B .   59 ?   12.912  61.584  38.000  0.00  0   B
-ATOM     2490    C   CD .  GLU   B .   59 ?   14.404  61.663  37.759  0.00  0   B
-ATOM     2491    O  OE1 .  GLU   B .   59 ?   14.831  61.607  36.581  0.00  0   B
-ATOM     2492    O  OE2 .  GLU   B .   59 ?   15.137  61.777  38.754 -1.07  0   B
-ATOM     3237    C    C .  ASP   B .  154 ?   17.708  57.721  41.604  0.00  0   B
-ATOM     3238    O    O .  ASP   B .  154 ?   17.212  58.730  41.018 -2.14  0   B
-ATOM     3239    C   CB .  ASP   B .  154 ?   15.520  56.620  41.941  0.00  0   B
-ATOM     3240    C   CG .  ASP   B .  154 ?   15.630  55.631  40.804  0.00  0   B
-ATOM     3241    O  OD1 .  ASP   B .  154 ?   16.754  55.332  40.331 -1.07  0   B
-ATOM     3242    O  OD2 .  ASP   B .  154 ?   14.601  55.095  40.376 -2.28  0   B
-ATOM     3245    C    C .  PHE   B .  155 ?   19.859  57.712  39.087  0.00  0   B
-ATOM     3246    O    O .  PHE   B .  155 ?   20.558  58.316  38.318 -3.21  0   B
-ATOM     3254    N    N .  GLY   B .  156 ?   19.098  56.710  38.688  0.00  0   B
-ATOM     3255    C   CA .  GLY   B .  156 ?   19.014  56.342  37.269  0.00  0   B
+ATOM    2389     N   NZ ?  LYS    Bxp 44 ?   17.801   61.554   36.438  -1.51  0 271 B
+ATOM    2454     O    O ?  GLU    Bxp 55 ?   11.608   61.345   33.284  -1.88  0 282 B
+ATOM    2485     C   CA ?  GLU    Bxp 59 ?   10.598   61.833   36.936   0.00  0 286 B
+ATOM    2488     C   CB ?  GLU    Bxp 59 ?   12.087   61.638   36.697   0.00  0 286 B
+ATOM    2489     C   CG ?  GLU    Bxp 59 ?   12.912   61.584   38.000   0.00  0 286 B
+ATOM    2490     C   CD ?  GLU    Bxp 59 ?   14.404   61.663   37.759   0.00  0 286 B
+ATOM    2491     O  OE1 ?  GLU    Bxp 59 ?   14.831   61.607   36.581   0.00  0 286 B
+ATOM    2492     O  OE2 ?  GLU    Bxp 59 ?   15.137   61.777   38.754  -1.07  0 286 B
+ATOM    3237     C    C ?  ASP    Bxp 154 ?   17.708   57.721   41.604   0.00  0 381 B
+ATOM    3238     O    O ?  ASP    Bxp 154 ?   17.212   58.730   41.018  -2.14  0 381 B
+ATOM    3239     C   CB ?  ASP    Bxp 154 ?   15.520   56.620   41.941   0.00  0 381 B
+ATOM    3240     C   CG ?  ASP    Bxp 154 ?   15.630   55.631   40.804   0.00  0 381 B
+ATOM    3241     O  OD1 ?  ASP    Bxp 154 ?   16.754   55.332   40.331  -1.07  0 381 B
+ATOM    3242     O  OD2 ?  ASP    Bxp 154 ?   14.601   55.095   40.376  -2.28  0 381 B
+ATOM    3245     C    C ?  PHE    Bxp 155 ?   19.859   57.712   39.087   0.00  0 382 B
+ATOM    3246     O    O ?  PHE    Bxp 155 ?   20.558   58.316   38.318  -3.21  0 382 B
+ATOM    3254     N    N ?  GLY    Bxp 156 ?   19.098   56.710   38.688   0.00  0 383 B
+ATOM    3255     C   CA ?  GLY    Bxp 156 ?   19.014   56.342   37.269   0.00  0 383 B
 #
--- a/tests/reference_output/123abc_out/pocket15_atm.cif
+++ b/tests/reference_output/123abc_out/pocket15_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    15:
 6  - Hydrophobicity Score              : 57.6667
 7  - Polarity Score                    :     0
 8  - Amino Acid based volume Score     : 3.5833
-9  - Pocket volume (Monte Carlo)       : 221.5000
+9  - Pocket volume (Monte Carlo)       : 222.3455
 10  -Pocket volume (convex hull)       : 14.5929
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 33.0000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,30 +37,31 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3639    C   CA .  ALA   B .  206 ?   25.485  44.511  57.685  0.00  0   B
-ATOM     2914    C  CD1 .  LEU   B .  113 ?   26.128  47.415  60.882  0.00  0   B
-ATOM     3642    C   CB .  ALA   B .  206 ?   24.633  43.235  57.872  0.00  0   B
-ATOM     3641    O    O .  ALA   B .  206 ?   27.664  43.745  58.449 -4.29  0   B
-ATOM     2922    C  CD1 .  LEU   B .  114 ?   18.369  46.670  63.743  0.00  0   B
-ATOM     3902    C   CD .  PRO   B .  238 ?   22.462  42.067  63.671  0.00  0   B
-ATOM     2892    O    O .  ALA   B .  110 ?   23.079  48.277  64.744 -3.21  0   B
-ATOM     3901    C   CG .  PRO   B .  238 ?   21.818  42.336  65.023  0.00  0   B
-ATOM     3919    C  CG2 .  VAL   B .  241 ?   18.754  43.171  62.407  0.00  0   B
-ATOM     2890    C   CA .  ALA   B .  110 ?   25.351  47.954  65.540  0.00  0   B
-ATOM     3918    C  CG1 .  VAL   B .  241 ?   19.352  42.826  59.944  0.00  0   B
-ATOM     3895    S   SG .  CYS   B .  237 ?   22.468  40.332  60.148  0.00  0   B
-ATOM     2893    C   CB .  ALA   B .  110 ?   25.301  47.008  66.740  0.00  0   B
-ATOM     2916    N    N .  LEU   B .  114 ?   21.229  49.545  62.399 -2.19  0   B
-ATOM     3889    O    O .  GLY   B .  236 ?   25.751  41.531  64.057  0.00  0   B
-ATOM     2912    C   CB .  LEU   B .  113 ?   24.074  48.764  61.348  0.00  0   B
-ATOM     2917    C   CA .  LEU   B .  114 ?   19.825  49.298  62.629  0.00  0   B
-ATOM     4130    C  CE1 .  PHE   B .  266 ?   16.326  46.124  60.459  0.00  0   B
-ATOM     2948    C   CB .  ALA   B .  117 ?   17.953  48.663  58.385  0.00  0   B
-ATOM     2910    C    C .  LEU   B .  113 ?   21.785  49.807  61.241  0.00  0   B
-ATOM     3891    C   CA .  CYS   B .  237 ?   24.487  40.444  62.093  0.00  0   B
-ATOM     2911    O    O .  LEU   B .  113 ?   21.152  49.905  60.239  0.00  0   B
-ATOM     3636    C  CG2 .  ILE   B .  205 ?   23.388  48.453  57.534  0.00  0   B
-ATOM     3602    O    O .  LEU   B .  202 ?   22.353  44.476  55.620 -1.07  0   B
-ATOM     3606    C  CD2 .  LEU   B .  202 ?   18.004  45.680  56.609  0.00  0   B
+ATOM    3639     C   CA ?  ALA    Bxp 206 ?   25.485   44.511   57.685   0.00  0 433 B
+ATOM    2914     C  CD1 ?  LEU    Bxp 113 ?   26.128   47.415   60.882   0.00  0 340 B
+ATOM    3642     C   CB ?  ALA    Bxp 206 ?   24.633   43.235   57.872   0.00  0 433 B
+ATOM    3641     O    O ?  ALA    Bxp 206 ?   27.664   43.745   58.449  -4.29  0 433 B
+ATOM    2922     C  CD1 ?  LEU    Bxp 114 ?   18.369   46.670   63.743   0.00  0 341 B
+ATOM    3902     C   CD ?  PRO    Bxp 238 ?   22.462   42.067   63.671   0.00  0 465 B
+ATOM    2892     O    O ?  ALA    Bxp 110 ?   23.079   48.277   64.744  -3.21  0 337 B
+ATOM    3901     C   CG ?  PRO    Bxp 238 ?   21.818   42.336   65.023   0.00  0 465 B
+ATOM    3919     C  CG2 ?  VAL    Bxp 241 ?   18.754   43.171   62.407   0.00  0 468 B
+ATOM    2890     C   CA ?  ALA    Bxp 110 ?   25.351   47.954   65.540   0.00  0 337 B
+ATOM    3918     C  CG1 ?  VAL    Bxp 241 ?   19.352   42.826   59.944   0.00  0 468 B
+ATOM    3895     S   SG ?  CYS    Bxp 237 ?   22.468   40.332   60.148   0.00  0 464 B
+ATOM    2893     C   CB ?  ALA    Bxp 110 ?   25.301   47.008   66.740   0.00  0 337 B
+ATOM    2916     N    N ?  LEU    Bxp 114 ?   21.229   49.545   62.399  -2.19  0 341 B
+ATOM    3889     O    O ?  GLY    Bxp 236 ?   25.751   41.531   64.057   0.00  0 463 B
+ATOM    2912     C   CB ?  LEU    Bxp 113 ?   24.074   48.764   61.348   0.00  0 340 B
+ATOM    2917     C   CA ?  LEU    Bxp 114 ?   19.825   49.298   62.629   0.00  0 341 B
+ATOM    4130     C  CE1 ?  PHE    Bxp 266 ?   16.326   46.124   60.459   0.00  0 493 B
+ATOM    2948     C   CB ?  ALA    Bxp 117 ?   17.953   48.663   58.385   0.00  0 344 B
+ATOM    2910     C    C ?  LEU    Bxp 113 ?   21.785   49.807   61.241   0.00  0 340 B
+ATOM    3891     C   CA ?  CYS    Bxp 237 ?   24.487   40.444   62.093   0.00  0 464 B
+ATOM    2911     O    O ?  LEU    Bxp 113 ?   21.152   49.905   60.239   0.00  0 340 B
+ATOM    3636     C  CG2 ?  ILE    Bxp 205 ?   23.388   48.453   57.534   0.00  0 432 B
+ATOM    3602     O    O ?  LEU    Bxp 202 ?   22.353   44.476   55.620  -1.07  0 429 B
+ATOM    3606     C  CD2 ?  LEU    Bxp 202 ?   18.004   45.680   56.609   0.00  0 429 B
 # 
--- a/tests/reference_output/123abc_out/pocket15_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket15_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,52 +15,53 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     2889    N    N .  ALA   B .  110 ?   26.627  48.705  65.568 -4.79  0   B
-ATOM     2890    C   CA .  ALA   B .  110 ?   25.351  47.954  65.540  0.00  0   B
-ATOM     2891    C    C .  ALA   B .  110 ?   24.009  48.706  65.482  0.00  0   B
-ATOM     2892    O    O .  ALA   B .  110 ?   23.079  48.277  64.744 -3.21  0   B
-ATOM     2893    C   CB .  ALA   B .  110 ?   25.301  47.008  66.740  0.00  0   B
-ATOM     2909    C   CA .  LEU   B .  113 ?   23.279  50.062  61.281  0.00  0   B
-ATOM     2910    C    C .  LEU   B .  113 ?   21.785  49.807  61.241  0.00  0   B
-ATOM     2911    O    O .  LEU   B .  113 ?   21.152  49.905  60.239  0.00  0   B
-ATOM     2912    C   CB .  LEU   B .  113 ?   24.074  48.764  61.348  0.00  0   B
-ATOM     2913    C   CG .  LEU   B .  113 ?   25.603  48.823  61.065  0.00  0   B
-ATOM     2914    C  CD1 .  LEU   B .  113 ?   26.128  47.415  60.882  0.00  0   B
-ATOM     2916    N    N .  LEU   B .  114 ?   21.229  49.545  62.399 -2.19  0   B
-ATOM     2917    C   CA .  LEU   B .  114 ?   19.825  49.298  62.629  0.00  0   B
-ATOM     2920    C   CB .  LEU   B .  114 ?   19.727  48.806  64.061  0.00  0   B
-ATOM     2921    C   CG .  LEU   B .  114 ?   18.632  47.903  64.623  0.00  0   B
-ATOM     2922    C  CD1 .  LEU   B .  114 ?   18.369  46.670  63.743  0.00  0   B
-ATOM     2923    C  CD2 .  LEU   B .  114 ?   19.208  47.511  65.968  0.00  0   B
-ATOM     2948    C   CB .  ALA   B .  117 ?   17.953  48.663  58.385  0.00  0   B
-ATOM     3600    C   CA .  LEU   B .  202 ?   20.271  44.948  54.579  0.00  0   B
-ATOM     3601    C    C .  LEU   B .  202 ?   21.600  44.222  54.708  0.00  0   B
-ATOM     3602    O    O .  LEU   B .  202 ?   22.353  44.476  55.620 -1.07  0   B
-ATOM     3603    C   CB .  LEU   B .  202 ?   19.212  44.020  55.190  0.00  0   B
-ATOM     3604    C   CG .  LEU   B .  202 ?   17.876  44.597  55.580  0.00  0   B
-ATOM     3606    C  CD2 .  LEU   B .  202 ?   18.004  45.680  56.609  0.00  0   B
-ATOM     3632    C    C .  ILE   B .  205 ?   25.327  46.616  56.447  0.00  0   B
-ATOM     3634    C   CB .  ILE   B .  205 ?   23.228  47.890  56.077  0.00  0   B
-ATOM     3636    C  CG2 .  ILE   B .  205 ?   23.388  48.453  57.534  0.00  0   B
-ATOM     3638    N    N .  ALA   B .  206 ?   24.907  45.366  56.637  0.00  0   B
-ATOM     3639    C   CA .  ALA   B .  206 ?   25.485  44.511  57.685  0.00  0   B
-ATOM     3640    C    C .  ALA   B .  206 ?   26.979  44.157  57.488  0.00  0   B
-ATOM     3641    O    O .  ALA   B .  206 ?   27.664  43.745  58.449 -4.29  0   B
-ATOM     3642    C   CB .  ALA   B .  206 ?   24.633  43.235  57.872  0.00  0   B
-ATOM     3888    C    C .  GLY   B .  236 ?   26.369  40.695  63.407  0.00  0   B
-ATOM     3889    O    O .  GLY   B .  236 ?   25.751  41.531  64.057  0.00  0   B
-ATOM     3890    N    N .  CYS   B .  237 ?   25.765  39.993  62.462  0.00  0   B
-ATOM     3891    C   CA .  CYS   B .  237 ?   24.487  40.444  62.093  0.00  0   B
-ATOM     3894    C   CB .  CYS   B .  237 ?   24.207  40.164  60.619  0.00  0   B
-ATOM     3895    S   SG .  CYS   B .  237 ?   22.468  40.332  60.148  0.00  0   B
-ATOM     3896    N    N .  PRO   B .  238 ?   22.623  40.597  63.684  0.00  0   B
-ATOM     3901    C   CG .  PRO   B .  238 ?   21.818  42.336  65.023  0.00  0   B
-ATOM     3902    C   CD .  PRO   B .  238 ?   22.462  42.067  63.671  0.00  0   B
-ATOM     3917    C   CB .  VAL   B .  241 ?   19.067  42.132  61.337  0.00  0   B
-ATOM     3918    C  CG1 .  VAL   B .  241 ?   19.352  42.826  59.944  0.00  0   B
-ATOM     3919    C  CG2 .  VAL   B .  241 ?   18.754  43.171  62.407  0.00  0   B
-ATOM     4128    C  CD1 .  PHE   B .  266 ?   15.519  46.953  61.239  0.00  0   B
-ATOM     4130    C  CE1 .  PHE   B .  266 ?   16.326  46.124  60.459  0.00  0   B
-ATOM     4132    C   CZ .  PHE   B .  266 ?   15.850  45.610  59.310  0.00  0   B
+ATOM    2889     N    N ?  ALA    Bxp 110 ?   26.627   48.705   65.568  -4.79  0 337 B
+ATOM    2890     C   CA ?  ALA    Bxp 110 ?   25.351   47.954   65.540   0.00  0 337 B
+ATOM    2891     C    C ?  ALA    Bxp 110 ?   24.009   48.706   65.482   0.00  0 337 B
+ATOM    2892     O    O ?  ALA    Bxp 110 ?   23.079   48.277   64.744  -3.21  0 337 B
+ATOM    2893     C   CB ?  ALA    Bxp 110 ?   25.301   47.008   66.740   0.00  0 337 B
+ATOM    2909     C   CA ?  LEU    Bxp 113 ?   23.279   50.062   61.281   0.00  0 340 B
+ATOM    2910     C    C ?  LEU    Bxp 113 ?   21.785   49.807   61.241   0.00  0 340 B
+ATOM    2911     O    O ?  LEU    Bxp 113 ?   21.152   49.905   60.239   0.00  0 340 B
+ATOM    2912     C   CB ?  LEU    Bxp 113 ?   24.074   48.764   61.348   0.00  0 340 B
+ATOM    2913     C   CG ?  LEU    Bxp 113 ?   25.603   48.823   61.065   0.00  0 340 B
+ATOM    2914     C  CD1 ?  LEU    Bxp 113 ?   26.128   47.415   60.882   0.00  0 340 B
+ATOM    2916     N    N ?  LEU    Bxp 114 ?   21.229   49.545   62.399  -2.19  0 341 B
+ATOM    2917     C   CA ?  LEU    Bxp 114 ?   19.825   49.298   62.629   0.00  0 341 B
+ATOM    2920     C   CB ?  LEU    Bxp 114 ?   19.727   48.806   64.061   0.00  0 341 B
+ATOM    2921     C   CG ?  LEU    Bxp 114 ?   18.632   47.903   64.623   0.00  0 341 B
+ATOM    2922     C  CD1 ?  LEU    Bxp 114 ?   18.369   46.670   63.743   0.00  0 341 B
+ATOM    2923     C  CD2 ?  LEU    Bxp 114 ?   19.208   47.511   65.968   0.00  0 341 B
+ATOM    2948     C   CB ?  ALA    Bxp 117 ?   17.953   48.663   58.385   0.00  0 344 B
+ATOM    3600     C   CA ?  LEU    Bxp 202 ?   20.271   44.948   54.579   0.00  0 429 B
+ATOM    3601     C    C ?  LEU    Bxp 202 ?   21.600   44.222   54.708   0.00  0 429 B
+ATOM    3602     O    O ?  LEU    Bxp 202 ?   22.353   44.476   55.620  -1.07  0 429 B
+ATOM    3603     C   CB ?  LEU    Bxp 202 ?   19.212   44.020   55.190   0.00  0 429 B
+ATOM    3604     C   CG ?  LEU    Bxp 202 ?   17.876   44.597   55.580   0.00  0 429 B
+ATOM    3606     C  CD2 ?  LEU    Bxp 202 ?   18.004   45.680   56.609   0.00  0 429 B
+ATOM    3632     C    C ?  ILE    Bxp 205 ?   25.327   46.616   56.447   0.00  0 432 B
+ATOM    3634     C   CB ?  ILE    Bxp 205 ?   23.228   47.890   56.077   0.00  0 432 B
+ATOM    3636     C  CG2 ?  ILE    Bxp 205 ?   23.388   48.453   57.534   0.00  0 432 B
+ATOM    3638     N    N ?  ALA    Bxp 206 ?   24.907   45.366   56.637   0.00  0 433 B
+ATOM    3639     C   CA ?  ALA    Bxp 206 ?   25.485   44.511   57.685   0.00  0 433 B
+ATOM    3640     C    C ?  ALA    Bxp 206 ?   26.979   44.157   57.488   0.00  0 433 B
+ATOM    3641     O    O ?  ALA    Bxp 206 ?   27.664   43.745   58.449  -4.29  0 433 B
+ATOM    3642     C   CB ?  ALA    Bxp 206 ?   24.633   43.235   57.872   0.00  0 433 B
+ATOM    3888     C    C ?  GLY    Bxp 236 ?   26.369   40.695   63.407   0.00  0 463 B
+ATOM    3889     O    O ?  GLY    Bxp 236 ?   25.751   41.531   64.057   0.00  0 463 B
+ATOM    3890     N    N ?  CYS    Bxp 237 ?   25.765   39.993   62.462   0.00  0 464 B
+ATOM    3891     C   CA ?  CYS    Bxp 237 ?   24.487   40.444   62.093   0.00  0 464 B
+ATOM    3894     C   CB ?  CYS    Bxp 237 ?   24.207   40.164   60.619   0.00  0 464 B
+ATOM    3895     S   SG ?  CYS    Bxp 237 ?   22.468   40.332   60.148   0.00  0 464 B
+ATOM    3896     N    N ?  PRO    Bxp 238 ?   22.623   40.597   63.684   0.00  0 465 B
+ATOM    3901     C   CG ?  PRO    Bxp 238 ?   21.818   42.336   65.023   0.00  0 465 B
+ATOM    3902     C   CD ?  PRO    Bxp 238 ?   22.462   42.067   63.671   0.00  0 465 B
+ATOM    3917     C   CB ?  VAL    Bxp 241 ?   19.067   42.132   61.337   0.00  0 468 B
+ATOM    3918     C  CG1 ?  VAL    Bxp 241 ?   19.352   42.826   59.944   0.00  0 468 B
+ATOM    3919     C  CG2 ?  VAL    Bxp 241 ?   18.754   43.171   62.407   0.00  0 468 B
+ATOM    4128     C  CD1 ?  PHE    Bxp 266 ?   15.519   46.953   61.239   0.00  0 493 B
+ATOM    4130     C  CE1 ?  PHE    Bxp 266 ?   16.326   46.124   60.459   0.00  0 493 B
+ATOM    4132     C   CZ ?  PHE    Bxp 266 ?   15.850   45.610   59.310   0.00  0 493 B
 #
--- a/tests/reference_output/123abc_out/pocket16_atm.cif
+++ b/tests/reference_output/123abc_out/pocket16_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    16:
 6  - Hydrophobicity Score              : 11.6923
 7  - Polarity Score                    :     9
 8  - Amino Acid based volume Score     : 4.5385
-9  - Pocket volume (Monte Carlo)       : 380.3267
+9  - Pocket volume (Monte Carlo)       : 372.5160
 10  -Pocket volume (convex hull)       : 34.1542
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 6.5000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,26 +37,27 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     7853    C   CA .  SER   D .  211 ?   42.974  31.063  42.423  0.00  0   D
-ATOM     7600    C  CH2 .  TRP   D .  178 ?   43.960  26.363  45.206  0.00  0   D
-ATOM     7847    O    O .  MET   D .  210 ?   44.036  29.741  40.141 -1.07  0   D
-ATOM     7857    O   OG .  SER   D .  211 ?   44.316  32.109  43.942  0.00  0   D
-ATOM     7598    C  CZ2 .  TRP   D .  178 ?   44.202  25.607  44.069  0.00  0   D
-ATOM     7864    C   CD .  PRO   D .  212 ?   41.974  28.366  43.102  0.00  0   D
-ATOM     7302    C   CB .  ARG   D .  140 ?   50.864  24.591  44.728  0.00  0   D
-ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
-ATOM     6936    N  ND2 .  ASN   D .   95 ?   54.321  26.577  41.672  0.00  0   D
-ATOM     6952    C  CD2 .  LEU   D .   97 ?   49.815  28.277  43.031  0.00  0   D
-ATOM     7493    O  OG1 .  THR   D .  165 ?   46.860  28.337  49.111 -0.95  0   D
-ATOM     7307    N  NH1 .  ARG   D .  140 ?   46.275  24.168  46.062  0.00  0   D
-ATOM     7304    C   CD .  ARG   D .  140 ?   49.165  24.333  46.741  0.00  0   D
-ATOM     7468    C   CE .  MET   D .  161 ?   51.743  26.507  49.224  0.00  0   D
-ATOM     6959    O  OD1 .  ASP   D .   98 ?   54.141  30.867  42.252 -4.02  0   D
-ATOM     7806    O  OE1 .  GLU   D .  204 ?   46.278  25.826  41.102 -2.14  0   D
-ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
-ATOM     6991    N  NH2 .  ARG   D .  101 ?   47.806  31.880  42.344 -2.61  0   D
-ATOM     6951    C  CD1 .  LEU   D .   97 ?   48.963  28.362  40.622  0.00  0   D
-ATOM     6990    N  NH1 .  ARG   D .  101 ?   49.983  32.573  42.931 -3.70  0   D
-ATOM     7467    S   SD .  MET   D .  161 ?   50.163  27.152  49.858  0.00  0   D
+ATOM    7853     C   CA ?  SER    Dxp 211 ?   42.974   31.063   42.423   0.00  0 438 D
+ATOM    7600     C  CH2 ?  TRP    Dxp 178 ?   43.960   26.363   45.206   0.00  0 405 D
+ATOM    7847     O    O ?  MET    Dxp 210 ?   44.036   29.741   40.141  -1.07  0 437 D
+ATOM    7857     O   OG ?  SER    Dxp 211 ?   44.316   32.109   43.942   0.00  0 438 D
+ATOM    7598     C  CZ2 ?  TRP    Dxp 178 ?   44.202   25.607   44.069   0.00  0 405 D
+ATOM    7864     C   CD ?  PRO    Dxp 212 ?   41.974   28.366   43.102   0.00  0 439 D
+ATOM    7302     C   CB ?  ARG    Dxp 140 ?   50.864   24.591   44.728   0.00  0 367 D
+ATOM    6415     N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM    6936     N  ND2 ?  ASN    Dxp 95 ?   54.321   26.577   41.672   0.00  0 322 D
+ATOM    6952     C  CD2 ?  LEU    Dxp 97 ?   49.815   28.277   43.031   0.00  0 324 D
+ATOM    7493     O  OG1 ?  THR    Dxp 165 ?   46.860   28.337   49.111  -0.95  0 392 D
+ATOM    7307     N  NH1 ?  ARG    Dxp 140 ?   46.275   24.168   46.062   0.00  0 367 D
+ATOM    7304     C   CD ?  ARG    Dxp 140 ?   49.165   24.333   46.741   0.00  0 367 D
+ATOM    7468     C   CE ?  MET    Dxp 161 ?   51.743   26.507   49.224   0.00  0 388 D
+ATOM    6959     O  OD1 ?  ASP    Dxp 98 ?   54.141   30.867   42.252  -4.02  0 325 D
+ATOM    7806     O  OE1 ?  GLU    Dxp 204 ?   46.278   25.826   41.102  -2.14  0 431 D
+ATOM    6960     O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM    6991     N  NH2 ?  ARG    Dxp 101 ?   47.806   31.880   42.344  -2.61  0 328 D
+ATOM    6951     C  CD1 ?  LEU    Dxp 97 ?   48.963   28.362   40.622   0.00  0 324 D
+ATOM    6990     N  NH1 ?  ARG    Dxp 101 ?   49.983   32.573   42.931  -3.70  0 328 D
+ATOM    7467     S   SD ?  MET    Dxp 161 ?   50.163   27.152   49.858   0.00  0 388 D
 # 
--- a/tests/reference_output/123abc_out/pocket16_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket16_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,50 +15,51 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     6412    C   CG .  GLN   D .   25 ?   57.187  27.871  48.035  0.00  0   D
-ATOM     6413    C   CD .  GLN   D .   25 ?   57.407  27.989  46.515  0.00  0   D
-ATOM     6415    N  NE2 .  GLN   D .   25 ?   56.420  27.531  45.718 -0.42  0   D
-ATOM     6934    C   CG .  ASN   D .   95 ?   55.423  26.157  42.216  0.00  0   D
-ATOM     6935    O  OD1 .  ASN   D .   95 ?   56.159  26.889  42.866 -2.14  0   D
-ATOM     6936    N  ND2 .  ASN   D .   95 ?   54.321  26.577  41.672  0.00  0   D
-ATOM     6949    C   CB .  LEU   D .   97 ?   51.235  27.362  41.089  0.00  0   D
-ATOM     6950    C   CG .  LEU   D .   97 ?   50.200  28.423  41.537  0.00  0   D
-ATOM     6951    C  CD1 .  LEU   D .   97 ?   48.963  28.362  40.622  0.00  0   D
-ATOM     6952    C  CD2 .  LEU   D .   97 ?   49.815  28.277  43.031  0.00  0   D
-ATOM     6958    C   CG .  ASP   D .   98 ?   55.143  30.209  41.861  0.00  0   D
-ATOM     6959    O  OD1 .  ASP   D .   98 ?   54.141  30.867  42.252 -4.02  0   D
-ATOM     6960    O  OD2 .  ASP   D .   98 ?   55.820  29.536  42.600 -2.55  0   D
-ATOM     6989    C   CZ .  ARG   D .  101 ?   49.039  32.250  41.984  0.00  0   D
-ATOM     6990    N  NH1 .  ARG   D .  101 ?   49.983  32.573  42.931 -3.70  0   D
-ATOM     6991    N  NH2 .  ARG   D .  101 ?   47.806  31.880  42.344 -2.61  0   D
-ATOM     7299    C   CA .  ARG   D .  140 ?   51.455  23.903  43.460  0.00  0   D
-ATOM     7302    C   CB .  ARG   D .  140 ?   50.864  24.591  44.728  0.00  0   D
-ATOM     7303    C   CG .  ARG   D .  140 ?   49.872  23.765  45.486  0.00  0   D
-ATOM     7304    C   CD .  ARG   D .  140 ?   49.165  24.333  46.741  0.00  0   D
-ATOM     7305    N   NE .  ARG   D .  140 ?   48.155  23.363  47.248  0.00  0   D
-ATOM     7306    C   CZ .  ARG   D .  140 ?   46.851  23.301  46.920  0.00  0   D
-ATOM     7307    N  NH1 .  ARG   D .  140 ?   46.275  24.168  46.062  0.00  0   D
-ATOM     7466    C   CG .  MET   D .  161 ?   50.568  27.737  51.524  0.00  0   D
-ATOM     7467    S   SD .  MET   D .  161 ?   50.163  27.152  49.858  0.00  0   D
-ATOM     7468    C   CE .  MET   D .  161 ?   51.743  26.507  49.224  0.00  0   D
-ATOM     7486    O  OD1 .  ASP   D .  164 ?   44.010  31.506  50.068  0.00  0   D
-ATOM     7492    C   CB .  THR   D .  165 ?   46.378  27.253  49.907  0.00  0   D
-ATOM     7493    O  OG1 .  THR   D .  165 ?   46.860  28.337  49.111 -0.95  0   D
-ATOM     7494    C  CG2 .  THR   D .  165 ?   46.295  26.043  49.013  0.00  0   D
-ATOM     7598    C  CZ2 .  TRP   D .  178 ?   44.202  25.607  44.069  0.00  0   D
-ATOM     7599    C  CZ3 .  TRP   D .  178 ?   43.261  25.813  46.311  0.00  0   D
-ATOM     7600    C  CH2 .  TRP   D .  178 ?   43.960  26.363  45.206  0.00  0   D
-ATOM     7805    C   CD .  GLU   D .  204 ?   45.509  25.019  40.553  0.00  0   D
-ATOM     7806    O  OE1 .  GLU   D .  204 ?   46.278  25.826  41.102 -2.14  0   D
-ATOM     7843    O    O .  GLY   D .  209 ?   46.861  31.370  39.639 -1.07  0   D
-ATOM     7846    C    C .  MET   D .  210 ?   43.952  30.964  40.187  0.00  0   D
-ATOM     7847    O    O .  MET   D .  210 ?   44.036  29.741  40.141 -1.07  0   D
-ATOM     7852    N    N .  SER   D .  211 ?   43.574  31.652  41.258 -1.51  0   D
-ATOM     7853    C   CA .  SER   D .  211 ?   42.974  31.063  42.423  0.00  0   D
-ATOM     7854    C    C .  SER   D .  211 ?   41.591  30.664  42.075  0.00  0   D
-ATOM     7856    C   CB .  SER   D .  211 ?   42.985  32.055  43.579  0.00  0   D
-ATOM     7857    O   OG .  SER   D .  211 ?   44.316  32.109  43.942  0.00  0   D
-ATOM     7858    N    N .  PRO   D .  212 ?   41.244  29.428  42.388  0.00  0   D
-ATOM     7864    C   CD .  PRO   D .  212 ?   41.974  28.366  43.102  0.00  0   D
+ATOM    6412     C   CG ?  GLN    Dxp 25 ?   57.187   27.871   48.035   0.00  0 252 D
+ATOM    6413     C   CD ?  GLN    Dxp 25 ?   57.407   27.989   46.515   0.00  0 252 D
+ATOM    6415     N  NE2 ?  GLN    Dxp 25 ?   56.420   27.531   45.718  -0.42  0 252 D
+ATOM    6934     C   CG ?  ASN    Dxp 95 ?   55.423   26.157   42.216   0.00  0 322 D
+ATOM    6935     O  OD1 ?  ASN    Dxp 95 ?   56.159   26.889   42.866  -2.14  0 322 D
+ATOM    6936     N  ND2 ?  ASN    Dxp 95 ?   54.321   26.577   41.672   0.00  0 322 D
+ATOM    6949     C   CB ?  LEU    Dxp 97 ?   51.235   27.362   41.089   0.00  0 324 D
+ATOM    6950     C   CG ?  LEU    Dxp 97 ?   50.200   28.423   41.537   0.00  0 324 D
+ATOM    6951     C  CD1 ?  LEU    Dxp 97 ?   48.963   28.362   40.622   0.00  0 324 D
+ATOM    6952     C  CD2 ?  LEU    Dxp 97 ?   49.815   28.277   43.031   0.00  0 324 D
+ATOM    6958     C   CG ?  ASP    Dxp 98 ?   55.143   30.209   41.861   0.00  0 325 D
+ATOM    6959     O  OD1 ?  ASP    Dxp 98 ?   54.141   30.867   42.252  -4.02  0 325 D
+ATOM    6960     O  OD2 ?  ASP    Dxp 98 ?   55.820   29.536   42.600  -2.55  0 325 D
+ATOM    6989     C   CZ ?  ARG    Dxp 101 ?   49.039   32.250   41.984   0.00  0 328 D
+ATOM    6990     N  NH1 ?  ARG    Dxp 101 ?   49.983   32.573   42.931  -3.70  0 328 D
+ATOM    6991     N  NH2 ?  ARG    Dxp 101 ?   47.806   31.880   42.344  -2.61  0 328 D
+ATOM    7299     C   CA ?  ARG    Dxp 140 ?   51.455   23.903   43.460   0.00  0 367 D
+ATOM    7302     C   CB ?  ARG    Dxp 140 ?   50.864   24.591   44.728   0.00  0 367 D
+ATOM    7303     C   CG ?  ARG    Dxp 140 ?   49.872   23.765   45.486   0.00  0 367 D
+ATOM    7304     C   CD ?  ARG    Dxp 140 ?   49.165   24.333   46.741   0.00  0 367 D
+ATOM    7305     N   NE ?  ARG    Dxp 140 ?   48.155   23.363   47.248   0.00  0 367 D
+ATOM    7306     C   CZ ?  ARG    Dxp 140 ?   46.851   23.301   46.920   0.00  0 367 D
+ATOM    7307     N  NH1 ?  ARG    Dxp 140 ?   46.275   24.168   46.062   0.00  0 367 D
+ATOM    7466     C   CG ?  MET    Dxp 161 ?   50.568   27.737   51.524   0.00  0 388 D
+ATOM    7467     S   SD ?  MET    Dxp 161 ?   50.163   27.152   49.858   0.00  0 388 D
+ATOM    7468     C   CE ?  MET    Dxp 161 ?   51.743   26.507   49.224   0.00  0 388 D
+ATOM    7486     O  OD1 ?  ASP    Dxp 164 ?   44.010   31.506   50.068   0.00  0 391 D
+ATOM    7492     C   CB ?  THR    Dxp 165 ?   46.378   27.253   49.907   0.00  0 392 D
+ATOM    7493     O  OG1 ?  THR    Dxp 165 ?   46.860   28.337   49.111  -0.95  0 392 D
+ATOM    7494     C  CG2 ?  THR    Dxp 165 ?   46.295   26.043   49.013   0.00  0 392 D
+ATOM    7598     C  CZ2 ?  TRP    Dxp 178 ?   44.202   25.607   44.069   0.00  0 405 D
+ATOM    7599     C  CZ3 ?  TRP    Dxp 178 ?   43.261   25.813   46.311   0.00  0 405 D
+ATOM    7600     C  CH2 ?  TRP    Dxp 178 ?   43.960   26.363   45.206   0.00  0 405 D
+ATOM    7805     C   CD ?  GLU    Dxp 204 ?   45.509   25.019   40.553   0.00  0 431 D
+ATOM    7806     O  OE1 ?  GLU    Dxp 204 ?   46.278   25.826   41.102  -2.14  0 431 D
+ATOM    7843     O    O ?  GLY    Dxp 209 ?   46.861   31.370   39.639  -1.07  0 436 D
+ATOM    7846     C    C ?  MET    Dxp 210 ?   43.952   30.964   40.187   0.00  0 437 D
+ATOM    7847     O    O ?  MET    Dxp 210 ?   44.036   29.741   40.141  -1.07  0 437 D
+ATOM    7852     N    N ?  SER    Dxp 211 ?   43.574   31.652   41.258  -1.51  0 438 D
+ATOM    7853     C   CA ?  SER    Dxp 211 ?   42.974   31.063   42.423   0.00  0 438 D
+ATOM    7854     C    C ?  SER    Dxp 211 ?   41.591   30.664   42.075   0.00  0 438 D
+ATOM    7856     C   CB ?  SER    Dxp 211 ?   42.985   32.055   43.579   0.00  0 438 D
+ATOM    7857     O   OG ?  SER    Dxp 211 ?   44.316   32.109   43.942   0.00  0 438 D
+ATOM    7858     N    N ?  PRO    Dxp 212 ?   41.244   29.428   42.388   0.00  0 439 D
+ATOM    7864     C   CD ?  PRO    Dxp 212 ?   41.974   28.366   43.102   0.00  0 439 D
 #
--- a/tests/reference_output/123abc_out/pocket17_atm.cif
+++ b/tests/reference_output/123abc_out/pocket17_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    17:
 6  - Hydrophobicity Score              : 12.0000
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.0000
-9  - Pocket volume (Monte Carlo)       : 154.0510
+9  - Pocket volume (Monte Carlo)       : 155.6925
 10  -Pocket volume (convex hull)       : 5.2942
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 0.0000
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,20 +37,21 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     3171    O    O .  GLY   B .  145 ?   24.279  62.076  57.870  0.00  0   B
-ATOM     2751    C  CE1 .  TYR   B .   93 ?   27.916  64.065  57.675  0.00  0   B
-ATOM     3181    N    N .  ASN   B .  147 ?   24.353  63.017  61.460 -3.03  0   B
-ATOM     3189    N    N .  HIS   B .  148 ?   23.808  60.293  60.791  0.00  0   B
-ATOM     2872    O  OE1 .  GLU   B .  107 ?   31.484  58.761  62.681 -0.95  0   B
-ATOM     2752    C  CE2 .  TYR   B .   93 ?   30.166  63.254  57.309  0.00  0   B
-ATOM     2873    O  OE2 .  GLU   B .  107 ?   29.348  59.201  62.656 -7.90  0   B
-ATOM     2754    O   OH .  TYR   B .   93 ?   29.703  64.823  59.044  0.00  0   B
-ATOM     2753    C   CZ .  TYR   B .   93 ?   29.259  64.044  58.017  0.00  0   B
-ATOM     2837    N    N .  ASN   B .  104 ?   33.994  55.404  60.098 -1.09  0   B
-ATOM     2835    C   CB .  CYS   B .  103 ?   31.652  54.686  58.227  0.00  0   B
-ATOM     2832    C   CA .  CYS   B .  103 ?   33.088  55.081  57.860  0.00  0   B
-ATOM     3198    N  NE2 .  HIS   B .  148 ?   27.061  57.958  62.310  0.00  0   B
-ATOM     2802    O   OH .  TYR   B .   99 ?   28.273  57.952  59.075 -7.50  0   B
-ATOM     2799    C  CE1 .  TYR   B .   99 ?   29.022  58.408  56.848  0.00  0   B
+ATOM    3171     O    O ?  GLY    Bxp 145 ?   24.279   62.076   57.870   0.00  0 372 B
+ATOM    2751     C  CE1 ?  TYR    Bxp 93 ?   27.916   64.065   57.675   0.00  0 320 B
+ATOM    3181     N    N ?  ASN    Bxp 147 ?   24.353   63.017   61.460  -3.03  0 374 B
+ATOM    3189     N    N ?  HIS    Bxp 148 ?   23.808   60.293   60.791   0.00  0 375 B
+ATOM    2872     O  OE1 ?  GLU    Bxp 107 ?   31.484   58.761   62.681  -0.95  0 334 B
+ATOM    2752     C  CE2 ?  TYR    Bxp 93 ?   30.166   63.254   57.309   0.00  0 320 B
+ATOM    2873     O  OE2 ?  GLU    Bxp 107 ?   29.348   59.201   62.656  -7.90  0 334 B
+ATOM    2754     O   OH ?  TYR    Bxp 93 ?   29.703   64.823   59.044   0.00  0 320 B
+ATOM    2753     C   CZ ?  TYR    Bxp 93 ?   29.259   64.044   58.017   0.00  0 320 B
+ATOM    2837     N    N ?  ASN    Bxp 104 ?   33.994   55.404   60.098  -1.09  0 331 B
+ATOM    2835     C   CB ?  CYS    Bxp 103 ?   31.652   54.686   58.227   0.00  0 330 B
+ATOM    2832     C   CA ?  CYS    Bxp 103 ?   33.088   55.081   57.860   0.00  0 330 B
+ATOM    3198     N  NE2 ?  HIS    Bxp 148 ?   27.061   57.958   62.310   0.00  0 375 B
+ATOM    2802     O   OH ?  TYR    Bxp 99 ?   28.273   57.952   59.075  -7.50  0 326 B
+ATOM    2799     C  CE1 ?  TYR    Bxp 99 ?   29.022   58.408   56.848   0.00  0 326 B
 # 
--- a/tests/reference_output/123abc_out/pocket17_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket17_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,39 +15,40 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     2748    C   CG .  TYR   B .   93 ?   28.347  62.433  55.906  0.00  0   B
-ATOM     2749    C  CD1 .  TYR   B .   93 ?   27.464  63.247  56.634  0.00  0   B
-ATOM     2750    C  CD2 .  TYR   B .   93 ?   29.699  62.458  56.235  0.00  0   B
-ATOM     2751    C  CE1 .  TYR   B .   93 ?   27.916  64.065  57.675  0.00  0   B
-ATOM     2752    C  CE2 .  TYR   B .   93 ?   30.166  63.254  57.309  0.00  0   B
-ATOM     2753    C   CZ .  TYR   B .   93 ?   29.259  64.044  58.017  0.00  0   B
-ATOM     2754    O   OH .  TYR   B .   93 ?   29.703  64.823  59.044  0.00  0   B
-ATOM     2797    C  CD1 .  TYR   B .   99 ?   29.075  58.066  55.512  0.00  0   B
-ATOM     2799    C  CE1 .  TYR   B .   99 ?   29.022  58.408  56.848  0.00  0   B
-ATOM     2801    C   CZ .  TYR   B .   99 ?   28.332  57.583  57.750  0.00  0   B
-ATOM     2802    O   OH .  TYR   B .   99 ?   28.273  57.952  59.075 -7.50  0   B
-ATOM     2832    C   CA .  CYS   B .  103 ?   33.088  55.081  57.860  0.00  0   B
-ATOM     2833    C    C .  CYS   B .  103 ?   34.047  54.644  59.003  0.00  0   B
-ATOM     2835    C   CB .  CYS   B .  103 ?   31.652  54.686  58.227  0.00  0   B
-ATOM     2837    N    N .  ASN   B .  104 ?   33.994  55.404  60.098 -1.09  0   B
-ATOM     2841    C   CB .  ASN   B .  104 ?   34.555  56.312  62.312  0.00  0   B
-ATOM     2871    C   CD .  GLU   B .  107 ?   30.339  58.618  63.162  0.00  0   B
-ATOM     2872    O  OE1 .  GLU   B .  107 ?   31.484  58.761  62.681 -0.95  0   B
-ATOM     2873    O  OE2 .  GLU   B .  107 ?   29.348  59.201  62.656 -7.90  0   B
-ATOM     2880    C  CG2 .  VAL   B .  108 ?   29.169  55.016  60.859  0.00  0   B
-ATOM     3170    C    C .  GLY   B .  145 ?   23.940  63.150  57.410  0.00  0   B
-ATOM     3171    O    O .  GLY   B .  145 ?   24.279  62.076  57.870  0.00  0   B
-ATOM     3173    C   CA .  GLU   B .  146 ?   24.527  64.377  59.465  0.00  0   B
-ATOM     3174    C    C .  GLU   B .  146 ?   23.693  63.539  60.431  0.00  0   B
-ATOM     3181    N    N .  ASN   B .  147 ?   24.353  63.017  61.460 -3.03  0   B
-ATOM     3182    C   CA .  ASN   B .  147 ?   23.727  62.121  62.392  0.00  0   B
-ATOM     3183    C    C .  ASN   B .  147 ?   23.179  60.827  61.846  0.00  0   B
-ATOM     3189    N    N .  HIS   B .  148 ?   23.808  60.293  60.791  0.00  0   B
-ATOM     3190    C   CA .  HIS   B .  148 ?   23.386  59.007  60.237  0.00  0   B
-ATOM     3194    C   CG .  HIS   B .  148 ?   24.910  57.903  61.905  0.00  0   B
-ATOM     3195    N  ND1 .  HIS   B .  148 ?   25.150  58.412  63.173  0.00  0   B
-ATOM     3196    C  CD2 .  HIS   B .  148 ?   26.118  57.632  61.362  0.00  0   B
-ATOM     3197    C  CE1 .  HIS   B .  148 ?   26.449  58.390  63.404  0.00  0   B
-ATOM     3198    N  NE2 .  HIS   B .  148 ?   27.061  57.958  62.310  0.00  0   B
+ATOM    2748     C   CG ?  TYR    Bxp 93 ?   28.347   62.433   55.906   0.00  0 320 B
+ATOM    2749     C  CD1 ?  TYR    Bxp 93 ?   27.464   63.247   56.634   0.00  0 320 B
+ATOM    2750     C  CD2 ?  TYR    Bxp 93 ?   29.699   62.458   56.235   0.00  0 320 B
+ATOM    2751     C  CE1 ?  TYR    Bxp 93 ?   27.916   64.065   57.675   0.00  0 320 B
+ATOM    2752     C  CE2 ?  TYR    Bxp 93 ?   30.166   63.254   57.309   0.00  0 320 B
+ATOM    2753     C   CZ ?  TYR    Bxp 93 ?   29.259   64.044   58.017   0.00  0 320 B
+ATOM    2754     O   OH ?  TYR    Bxp 93 ?   29.703   64.823   59.044   0.00  0 320 B
+ATOM    2797     C  CD1 ?  TYR    Bxp 99 ?   29.075   58.066   55.512   0.00  0 326 B
+ATOM    2799     C  CE1 ?  TYR    Bxp 99 ?   29.022   58.408   56.848   0.00  0 326 B
+ATOM    2801     C   CZ ?  TYR    Bxp 99 ?   28.332   57.583   57.750   0.00  0 326 B
+ATOM    2802     O   OH ?  TYR    Bxp 99 ?   28.273   57.952   59.075  -7.50  0 326 B
+ATOM    2832     C   CA ?  CYS    Bxp 103 ?   33.088   55.081   57.860   0.00  0 330 B
+ATOM    2833     C    C ?  CYS    Bxp 103 ?   34.047   54.644   59.003   0.00  0 330 B
+ATOM    2835     C   CB ?  CYS    Bxp 103 ?   31.652   54.686   58.227   0.00  0 330 B
+ATOM    2837     N    N ?  ASN    Bxp 104 ?   33.994   55.404   60.098  -1.09  0 331 B
+ATOM    2841     C   CB ?  ASN    Bxp 104 ?   34.555   56.312   62.312   0.00  0 331 B
+ATOM    2871     C   CD ?  GLU    Bxp 107 ?   30.339   58.618   63.162   0.00  0 334 B
+ATOM    2872     O  OE1 ?  GLU    Bxp 107 ?   31.484   58.761   62.681  -0.95  0 334 B
+ATOM    2873     O  OE2 ?  GLU    Bxp 107 ?   29.348   59.201   62.656  -7.90  0 334 B
+ATOM    2880     C  CG2 ?  VAL    Bxp 108 ?   29.169   55.016   60.859   0.00  0 335 B
+ATOM    3170     C    C ?  GLY    Bxp 145 ?   23.940   63.150   57.410   0.00  0 372 B
+ATOM    3171     O    O ?  GLY    Bxp 145 ?   24.279   62.076   57.870   0.00  0 372 B
+ATOM    3173     C   CA ?  GLU    Bxp 146 ?   24.527   64.377   59.465   0.00  0 373 B
+ATOM    3174     C    C ?  GLU    Bxp 146 ?   23.693   63.539   60.431   0.00  0 373 B
+ATOM    3181     N    N ?  ASN    Bxp 147 ?   24.353   63.017   61.460  -3.03  0 374 B
+ATOM    3182     C   CA ?  ASN    Bxp 147 ?   23.727   62.121   62.392   0.00  0 374 B
+ATOM    3183     C    C ?  ASN    Bxp 147 ?   23.179   60.827   61.846   0.00  0 374 B
+ATOM    3189     N    N ?  HIS    Bxp 148 ?   23.808   60.293   60.791   0.00  0 375 B
+ATOM    3190     C   CA ?  HIS    Bxp 148 ?   23.386   59.007   60.237   0.00  0 375 B
+ATOM    3194     C   CG ?  HIS    Bxp 148 ?   24.910   57.903   61.905   0.00  0 375 B
+ATOM    3195     N  ND1 ?  HIS    Bxp 148 ?   25.150   58.412   63.173   0.00  0 375 B
+ATOM    3196     C  CD2 ?  HIS    Bxp 148 ?   26.118   57.632   61.362   0.00  0 375 B
+ATOM    3197     C  CE1 ?  HIS    Bxp 148 ?   26.449   58.390   63.404   0.00  0 375 B
+ATOM    3198     N  NE2 ?  HIS    Bxp 148 ?   27.061   57.958   62.310   0.00  0 375 B
 #
--- a/tests/reference_output/123abc_out/pocket18_atm.cif
+++ b/tests/reference_output/123abc_out/pocket18_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    18:
 6  - Hydrophobicity Score              : 53.6000
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 4.0000
-9  - Pocket volume (Monte Carlo)       : 282.0984
+9  - Pocket volume (Monte Carlo)       : 286.0757
 10  -Pocket volume (convex hull)       : 22.1820
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 17.8947
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,28 +37,29 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     1359    O    O .  LEU   A .  184 ?   14.349  39.319  26.613 -1.07  0   A
-ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
-ATOM     1363    C  CD2 .  LEU   A .  184 ?   17.375  37.076  23.709  0.00  0   A
-ATOM     3351    N    N .  ALA   B .  170 ?   17.691  42.856  27.354 -6.98  0   B
-ATOM     3340    C   CB .  ALA   B .  168 ?   22.786  43.694  28.595  0.00  0   B
-ATOM     1640    O    O .  SER   A .  219 ?   23.891  43.579  25.385 -1.07  0   A
-ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
-ATOM     1632    O    O .  LEU   A .  218 ?   23.990  39.840  23.886  0.00  0   A
-ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
-ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
-ATOM     1298    C  CD1 .  ILE   A .  176 ?   20.379  35.378  24.896  0.00  0   A
-ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
-ATOM     1279    C  CD1 .  PHE   A .  174 ?   15.732  32.610  26.953  0.00  0   A
-ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
-ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
-ATOM     1297    C  CG2 .  ILE   A .  176 ?   21.592  37.080  22.335  0.00  0   A
-ATOM     1663    C   CB .  TYR   A .  222 ?   18.792  43.075  23.036  0.00  0   A
-ATOM     1659    N    N .  TYR   A .  222 ?   20.759  42.581  21.578 -1.09  0   A
-ATOM     1362    C  CD1 .  LEU   A .  184 ?   17.407  38.949  21.882  0.00  0   A
-ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
-ATOM     1357    C   CA .  LEU   A .  184 ?   14.567  38.323  24.463  0.00  0   A
-ATOM     1353    O    O .  SER   A .  183 ?   12.402  36.556  25.117  0.00  0   A
-ATOM     1360    C   CB .  LEU   A .  184 ?   15.704  39.018  23.710  0.00  0   A
+ATOM    1359     O    O ?  LEU    Axp 184 ?   14.349   39.319   26.613  -1.07  0 411 A
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    1363     C  CD2 ?  LEU    Axp 184 ?   17.375   37.076   23.709   0.00  0 411 A
+ATOM    3351     N    N ?  ALA    Bxp 170 ?   17.691   42.856   27.354  -6.98  0 397 B
+ATOM    3340     C   CB ?  ALA    Bxp 168 ?   22.786   43.694   28.595   0.00  0 395 B
+ATOM    1640     O    O ?  SER    Axp 219 ?   23.891   43.579   25.385  -1.07  0 446 A
+ATOM    1638     C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM    1632     O    O ?  LEU    Axp 218 ?   23.990   39.840   23.886   0.00  0 445 A
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    3338     C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM    1298     C  CD1 ?  ILE    Axp 176 ?   20.379   35.378   24.896   0.00  0 403 A
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    1279     C  CD1 ?  PHE    Axp 174 ?   15.732   32.610   26.953   0.00  0 401 A
+ATOM    1244     C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM    3342     C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM    1297     C  CG2 ?  ILE    Axp 176 ?   21.592   37.080   22.335   0.00  0 403 A
+ATOM    1663     C   CB ?  TYR    Axp 222 ?   18.792   43.075   23.036   0.00  0 449 A
+ATOM    1659     N    N ?  TYR    Axp 222 ?   20.759   42.581   21.578  -1.09  0 449 A
+ATOM    1362     C  CD1 ?  LEU    Axp 184 ?   17.407   38.949   21.882   0.00  0 411 A
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    1357     C   CA ?  LEU    Axp 184 ?   14.567   38.323   24.463   0.00  0 411 A
+ATOM    1353     O    O ?  SER    Axp 183 ?   12.402   36.556   25.117   0.00  0 410 A
+ATOM    1360     C   CB ?  LEU    Axp 184 ?   15.704   39.018   23.710   0.00  0 411 A
 # 
--- a/tests/reference_output/123abc_out/pocket18_env_atm.cif
+++ b/tests/reference_output/123abc_out/pocket18_env_atm.cif
@@ -8,7 +8,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -16,60 +15,61 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     1237    C    C .  ALA   A .  168 ?   20.392  32.949  30.818  0.00  0   A
-ATOM     1238    O    O .  ALA   A .  168 ?   20.773  34.081  30.515  0.00  0   A
-ATOM     1241    C   CA .  HIS   A .  169 ?   18.086  33.603  31.255  0.00  0   A
-ATOM     1244    C   CB .  HIS   A .  169 ?   17.333  33.968  29.971  0.00  0   A
-ATOM     1245    C   CG .  HIS   A .  169 ?   16.104  34.797  30.229  0.00  0   A
-ATOM     1246    N  ND1 .  HIS   A .  169 ?   14.891  34.244  30.609  0.00  0   A
-ATOM     1247    C  CD2 .  HIS   A .  169 ?   15.907  36.141  30.193  0.00  0   A
-ATOM     1248    C  CE1 .  HIS   A .  169 ?   14.000  35.208  30.775  0.00  0   A
-ATOM     1249    N  NE2 .  HIS   A .  169 ?   14.590  36.367  30.529  0.00  0   A
-ATOM     1277    C   CB .  PHE   A .  174 ?   17.509  31.996  25.288  0.00  0   A
-ATOM     1278    C   CG .  PHE   A .  174 ?   16.182  31.763  25.962  0.00  0   A
-ATOM     1279    C  CD1 .  PHE   A .  174 ?   15.732  32.610  26.953  0.00  0   A
-ATOM     1281    C  CE1 .  PHE   A .  174 ?   14.531  32.366  27.594  0.00  0   A
-ATOM     1295    C   CB .  ILE   A .  176 ?   21.717  35.588  22.696  0.00  0   A
-ATOM     1296    C  CG1 .  ILE   A .  176 ?   21.726  35.377  24.235  0.00  0   A
-ATOM     1297    C  CG2 .  ILE   A .  176 ?   21.592  37.080  22.335  0.00  0   A
-ATOM     1298    C  CD1 .  ILE   A .  176 ?   20.379  35.378  24.896  0.00  0   A
-ATOM     1352    C    C .  SER   A .  183 ?   12.496  37.011  23.965  0.00  0   A
-ATOM     1353    O    O .  SER   A .  183 ?   12.402  36.556  25.117  0.00  0   A
-ATOM     1356    N    N .  LEU   A .  184 ?   13.536  37.768  23.548  0.00  0   A
-ATOM     1357    C   CA .  LEU   A .  184 ?   14.567  38.323  24.463  0.00  0   A
-ATOM     1358    C    C .  LEU   A .  184 ?   13.995  39.330  25.444  0.00  0   A
-ATOM     1359    O    O .  LEU   A .  184 ?   14.349  39.319  26.613 -1.07  0   A
-ATOM     1360    C   CB .  LEU   A .  184 ?   15.704  39.018  23.710  0.00  0   A
-ATOM     1361    C   CG .  LEU   A .  184 ?   16.583  38.094  22.866  0.00  0   A
-ATOM     1362    C  CD1 .  LEU   A .  184 ?   17.407  38.949  21.882  0.00  0   A
-ATOM     1363    C  CD2 .  LEU   A .  184 ?   17.375  37.076  23.709  0.00  0   A
-ATOM     1387    O  OD1 .  ASN   A .  187 ?   11.727  35.895  28.835 -1.07  0   A
-ATOM     1631    C    C .  LEU   A .  218 ?   25.155  39.717  24.180  0.00  0   A
-ATOM     1632    O    O .  LEU   A .  218 ?   23.990  39.840  23.886  0.00  0   A
-ATOM     1637    N    N .  SER   A .  219 ?   25.769  40.519  25.023  0.00  0   A
-ATOM     1638    C   CA .  SER   A .  219 ?   25.023  41.475  25.807  0.00  0   A
-ATOM     1639    C    C .  SER   A .  219 ?   24.704  42.744  24.987  0.00  0   A
-ATOM     1640    O    O .  SER   A .  219 ?   23.891  43.579  25.385 -1.07  0   A
-ATOM     1641    C   CB .  SER   A .  219 ?   25.796  41.724  27.105  0.00  0   A
-ATOM     1656    C   CB .  VAL   A .  221 ?   22.834  40.427  20.388  0.00  0   A
-ATOM     1659    N    N .  TYR   A .  222 ?   20.759  42.581  21.578 -1.09  0   A
-ATOM     1660    C   CA .  TYR   A .  222 ?   19.471  43.262  21.673  0.00  0   A
-ATOM     1663    C   CB .  TYR   A .  222 ?   18.792  43.075  23.036  0.00  0   A
-ATOM     1664    C   CG .  TYR   A .  222 ?   17.328  43.572  23.026  0.00  0   A
-ATOM     1665    C  CD1 .  TYR   A .  222 ?   16.254  42.671  22.864  0.00  0   A
-ATOM     3337    C   CA .  ALA   B .  168 ?   22.105  43.779  29.982  0.00  0   B
-ATOM     3338    C    C .  ALA   B .  168 ?   20.955  42.763  30.104  0.00  0   B
-ATOM     3339    O    O .  ALA   B .  168 ?   21.154  41.582  30.397  0.00  0   B
-ATOM     3340    C   CB .  ALA   B .  168 ?   22.786  43.694  28.595  0.00  0   B
-ATOM     3341    N    N .  HIS   B .  169 ?   19.743  43.280  29.949  0.00  0   B
-ATOM     3342    C   CA .  HIS   B .  169 ?   18.586  42.470  29.578  0.00  0   B
-ATOM     3343    C    C .  HIS   B .  169 ?   17.666  43.282  28.628  0.00  0   B
-ATOM     3345    C   CB .  HIS   B .  169 ?   17.804  41.919  30.765  0.00  0   B
-ATOM     3346    C   CG .  HIS   B .  169 ?   16.549  41.202  30.364  0.00  0   B
-ATOM     3348    C  CD2 .  HIS   B .  169 ?   16.267  39.878  30.268  0.00  0   B
-ATOM     3350    N  NE2 .  HIS   B .  169 ?   14.959  39.769  29.859  0.00  0   B
-ATOM     3351    N    N .  ALA   B .  170 ?   17.691  42.856  27.354 -6.98  0   B
-ATOM     3352    C   CA .  ALA   B .  170 ?   16.780  43.344  26.347  0.00  0   B
-ATOM     3355    C   CB .  ALA   B .  170 ?   15.447  42.648  26.503  0.00  0   B
+ATOM    1237     C    C ?  ALA    Axp 168 ?   20.392   32.949   30.818   0.00  0 395 A
+ATOM    1238     O    O ?  ALA    Axp 168 ?   20.773   34.081   30.515   0.00  0 395 A
+ATOM    1241     C   CA ?  HIS    Axp 169 ?   18.086   33.603   31.255   0.00  0 396 A
+ATOM    1244     C   CB ?  HIS    Axp 169 ?   17.333   33.968   29.971   0.00  0 396 A
+ATOM    1245     C   CG ?  HIS    Axp 169 ?   16.104   34.797   30.229   0.00  0 396 A
+ATOM    1246     N  ND1 ?  HIS    Axp 169 ?   14.891   34.244   30.609   0.00  0 396 A
+ATOM    1247     C  CD2 ?  HIS    Axp 169 ?   15.907   36.141   30.193   0.00  0 396 A
+ATOM    1248     C  CE1 ?  HIS    Axp 169 ?   14.000   35.208   30.775   0.00  0 396 A
+ATOM    1249     N  NE2 ?  HIS    Axp 169 ?   14.590   36.367   30.529   0.00  0 396 A
+ATOM    1277     C   CB ?  PHE    Axp 174 ?   17.509   31.996   25.288   0.00  0 401 A
+ATOM    1278     C   CG ?  PHE    Axp 174 ?   16.182   31.763   25.962   0.00  0 401 A
+ATOM    1279     C  CD1 ?  PHE    Axp 174 ?   15.732   32.610   26.953   0.00  0 401 A
+ATOM    1281     C  CE1 ?  PHE    Axp 174 ?   14.531   32.366   27.594   0.00  0 401 A
+ATOM    1295     C   CB ?  ILE    Axp 176 ?   21.717   35.588   22.696   0.00  0 403 A
+ATOM    1296     C  CG1 ?  ILE    Axp 176 ?   21.726   35.377   24.235   0.00  0 403 A
+ATOM    1297     C  CG2 ?  ILE    Axp 176 ?   21.592   37.080   22.335   0.00  0 403 A
+ATOM    1298     C  CD1 ?  ILE    Axp 176 ?   20.379   35.378   24.896   0.00  0 403 A
+ATOM    1352     C    C ?  SER    Axp 183 ?   12.496   37.011   23.965   0.00  0 410 A
+ATOM    1353     O    O ?  SER    Axp 183 ?   12.402   36.556   25.117   0.00  0 410 A
+ATOM    1356     N    N ?  LEU    Axp 184 ?   13.536   37.768   23.548   0.00  0 411 A
+ATOM    1357     C   CA ?  LEU    Axp 184 ?   14.567   38.323   24.463   0.00  0 411 A
+ATOM    1358     C    C ?  LEU    Axp 184 ?   13.995   39.330   25.444   0.00  0 411 A
+ATOM    1359     O    O ?  LEU    Axp 184 ?   14.349   39.319   26.613  -1.07  0 411 A
+ATOM    1360     C   CB ?  LEU    Axp 184 ?   15.704   39.018   23.710   0.00  0 411 A
+ATOM    1361     C   CG ?  LEU    Axp 184 ?   16.583   38.094   22.866   0.00  0 411 A
+ATOM    1362     C  CD1 ?  LEU    Axp 184 ?   17.407   38.949   21.882   0.00  0 411 A
+ATOM    1363     C  CD2 ?  LEU    Axp 184 ?   17.375   37.076   23.709   0.00  0 411 A
+ATOM    1387     O  OD1 ?  ASN    Axp 187 ?   11.727   35.895   28.835  -1.07  0 414 A
+ATOM    1631     C    C ?  LEU    Axp 218 ?   25.155   39.717   24.180   0.00  0 445 A
+ATOM    1632     O    O ?  LEU    Axp 218 ?   23.990   39.840   23.886   0.00  0 445 A
+ATOM    1637     N    N ?  SER    Axp 219 ?   25.769   40.519   25.023   0.00  0 446 A
+ATOM    1638     C   CA ?  SER    Axp 219 ?   25.023   41.475   25.807   0.00  0 446 A
+ATOM    1639     C    C ?  SER    Axp 219 ?   24.704   42.744   24.987   0.00  0 446 A
+ATOM    1640     O    O ?  SER    Axp 219 ?   23.891   43.579   25.385  -1.07  0 446 A
+ATOM    1641     C   CB ?  SER    Axp 219 ?   25.796   41.724   27.105   0.00  0 446 A
+ATOM    1656     C   CB ?  VAL    Axp 221 ?   22.834   40.427   20.388   0.00  0 448 A
+ATOM    1659     N    N ?  TYR    Axp 222 ?   20.759   42.581   21.578  -1.09  0 449 A
+ATOM    1660     C   CA ?  TYR    Axp 222 ?   19.471   43.262   21.673   0.00  0 449 A
+ATOM    1663     C   CB ?  TYR    Axp 222 ?   18.792   43.075   23.036   0.00  0 449 A
+ATOM    1664     C   CG ?  TYR    Axp 222 ?   17.328   43.572   23.026   0.00  0 449 A
+ATOM    1665     C  CD1 ?  TYR    Axp 222 ?   16.254   42.671   22.864   0.00  0 449 A
+ATOM    3337     C   CA ?  ALA    Bxp 168 ?   22.105   43.779   29.982   0.00  0 395 B
+ATOM    3338     C    C ?  ALA    Bxp 168 ?   20.955   42.763   30.104   0.00  0 395 B
+ATOM    3339     O    O ?  ALA    Bxp 168 ?   21.154   41.582   30.397   0.00  0 395 B
+ATOM    3340     C   CB ?  ALA    Bxp 168 ?   22.786   43.694   28.595   0.00  0 395 B
+ATOM    3341     N    N ?  HIS    Bxp 169 ?   19.743   43.280   29.949   0.00  0 396 B
+ATOM    3342     C   CA ?  HIS    Bxp 169 ?   18.586   42.470   29.578   0.00  0 396 B
+ATOM    3343     C    C ?  HIS    Bxp 169 ?   17.666   43.282   28.628   0.00  0 396 B
+ATOM    3345     C   CB ?  HIS    Bxp 169 ?   17.804   41.919   30.765   0.00  0 396 B
+ATOM    3346     C   CG ?  HIS    Bxp 169 ?   16.549   41.202   30.364   0.00  0 396 B
+ATOM    3348     C  CD2 ?  HIS    Bxp 169 ?   16.267   39.878   30.268   0.00  0 396 B
+ATOM    3350     N  NE2 ?  HIS    Bxp 169 ?   14.959   39.769   29.859   0.00  0 396 B
+ATOM    3351     N    N ?  ALA    Bxp 170 ?   17.691   42.856   27.354  -6.98  0 397 B
+ATOM    3352     C   CA ?  ALA    Bxp 170 ?   16.780   43.344   26.347   0.00  0 397 B
+ATOM    3355     C   CB ?  ALA    Bxp 170 ?   15.447   42.648   26.503   0.00  0 397 B
 #
--- a/tests/reference_output/123abc_out/pocket19_atm.cif
+++ b/tests/reference_output/123abc_out/pocket19_atm.cif
@@ -15,7 +15,7 @@ Information about the pocket    19:
 6  - Hydrophobicity Score              : 62.1111
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 4.3333
-9  - Pocket volume (Monte Carlo)       : 430.3055
+9  - Pocket volume (Monte Carlo)       : 433.0316
 10  -Pocket volume (convex hull)       : 67.6357
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 28.1176
@@ -30,7 +30,6 @@ _atom_site.label_atom_id
 _atom_site.label_alt_id
 _atom_site.label_comp_id
 _atom_site.label_asym_id
-_atom_site.label_entity_id
 _atom_site.label_seq_id
 _atom_site.pdbx_PDB_ins_code
 _atom_site.Cartn_x
@@ -38,37 +37,38 @@ _atom_site.Cartn_y
 _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
 _atom_site.auth_asym_id
-ATOM     7944    C   CZ .  TYR   D .  222 ?   28.663  18.750  51.374  0.00  0   D
-ATOM     7943    C  CE2 .  TYR   D .  222 ?   27.884  19.861  51.731  0.00  0   D
-ATOM     7945    O   OH .  TYR   D .  222 ?   28.142  17.449  51.358 -4.29  0   D
-ATOM     7647    C   CB .  ALA   D .  185 ?   30.355  15.757  53.617  0.00  0   D
-ATOM     7644    C   CA .  ALA   D .  185 ?   31.641  16.003  54.405  0.00  0   D
-ATOM     7942    C  CE1 .  TYR   D .  222 ?   29.998  18.906  51.064  0.00  0   D
-ATOM     7940    C  CD1 .  TYR   D .  222 ?   30.563  20.141  51.099  0.00  0   D
-ATOM     7941    C  CD2 .  TYR   D .  222 ?   28.465  21.119  51.770  0.00  0   D
-ATOM     7577    C  CD1 .  ILE   D .  176 ?   37.672  25.382  53.690  0.00  0   D
-ATOM     7576    C  CG2 .  ILE   D .  176 ?   36.592  24.562  50.949  0.00  0   D
-ATOM     7575    C  CG1 .  ILE   D .  176 ?   38.212  24.231  52.898  0.00  0   D
-ATOM     7642    C  CD2 .  LEU   D .  184 ?   36.369  20.233  52.078  0.00  0   D
-ATOM     7641    C  CD1 .  LEU   D .  184 ?   34.448  20.808  50.650  0.00  0   D
-ATOM     7938    C   CB .  TYR   D .  222 ?   30.486  22.638  51.402  0.00  0   D
-ATOM     7934    N    N .  TYR   D .  222 ?   31.202  24.455  49.938 -1.09  0   D
-ATOM     7907    O    O .  LEU   D .  218 ?   34.008  27.525  52.271 -0.40  0   D
-ATOM     7639    C   CB .  LEU   D .  184 ?   34.244  18.838  52.215  0.00  0   D
-ATOM     7939    C   CG .  TYR   D .  222 ?   29.832  21.273  51.448  0.00  0   D
-ATOM     7560    C  CE1 .  PHE   D .  174 ?   39.595  17.433  56.140  0.00  0   D
-ATOM     7638    O    O .  LEU   D .  184 ?   33.870  17.251  55.188  0.00  0   D
-ATOM     7525    N  ND1 .  HIS   D .  169 ?   36.365  20.155  60.429 -1.93  0   D
-ATOM     7558    C  CD1 .  PHE   D .  174 ?   39.696  18.611  55.390  0.00  0   D
-ATOM     7524    C   CG .  HIS   D .  169 ?   36.743  21.442  60.097  0.00  0   D
-ATOM     7527    C  CE1 .  HIS   D .  169 ?   35.170  20.180  60.996  0.00  0   D
-ATOM     7528    N  NE2 .  HIS   D .  169 ?   34.778  21.438  61.089  0.00  0   D
-ATOM     7526    C  CD2 .  HIS   D .  169 ?   35.750  22.249  60.547  0.00  0   D
-ATOM     7637    C    C .  LEU   D .  184 ?   33.727  17.072  53.991  0.00  0   D
-ATOM     7523    C   CB .  HIS   D .  169 ?   38.074  21.770  59.468  0.00  0   D
-ATOM     7556    C   CB .  PHE   D .  174 ?   40.965  20.182  53.857  0.00  0   D
-ATOM     7513    C  CG2 .  THR   D .  167 ?   39.795  26.405  56.782  0.00  0   D
-ATOM     7510    O    O .  THR   D .  167 ?   41.927  23.289  56.784  0.00  0   D
-ATOM     7517    O    O .  ALA   D .  168 ?   40.187  24.764  60.121 -3.35  0   D
+ATOM    7944     C   CZ ?  TYR    Dxp 222 ?   28.663   18.750   51.374   0.00  0 449 D
+ATOM    7943     C  CE2 ?  TYR    Dxp 222 ?   27.884   19.861   51.731   0.00  0 449 D
+ATOM    7945     O   OH ?  TYR    Dxp 222 ?   28.142   17.449   51.358  -4.29  0 449 D
+ATOM    7647     C   CB ?  ALA    Dxp 185 ?   30.355   15.757   53.617   0.00  0 412 D
+ATOM    7644     C   CA ?  ALA    Dxp 185 ?   31.641   16.003   54.405   0.00  0 412 D
+ATOM    7942     C  CE1 ?  TYR    Dxp 222 ?   29.998   18.906   51.064   0.00  0 449 D
+ATOM    7940     C  CD1 ?  TYR    Dxp 222 ?   30.563   20.141   51.099   0.00  0 449 D
+ATOM    7941     C  CD2 ?  TYR    Dxp 222 ?   28.465   21.119   51.770   0.00  0 449 D
+ATOM    7577     C  CD1 ?  ILE    Dxp 176 ?   37.672   25.382   53.690   0.00  0 403 D
+ATOM    7576     C  CG2 ?  ILE    Dxp 176 ?   36.592   24.562   50.949   0.00  0 403 D
+ATOM    7575     C  CG1 ?  ILE    Dxp 176 ?   38.212   24.231   52.898   0.00  0 403 D
+ATOM    7642     C  CD2 ?  LEU    Dxp 184 ?   36.369   20.233   52.078   0.00  0 411 D
+ATOM    7641     C  CD1 ?  LEU    Dxp 184 ?   34.448   20.808   50.650   0.00  0 411 D
+ATOM    7938     C   CB ?  TYR    Dxp 222 ?   30.486   22.638   51.402   0.00  0 449 D
+ATOM    7934     N    N ?  TYR    Dxp 222 ?   31.202   24.455   49.938  -1.09  0 449 D
+ATOM    7907     O    O ?  LEU    Dxp 218 ?   34.008   27.525   52.271  -0.40  0 445 D
+ATOM    7639     C   CB ?  LEU    Dxp 184 ?   34.244   18.838   52.215   0.00  0 411 D
+ATOM    7939     C   CG ?  TYR    Dxp 222 ?   29.832   21.273   51.448   0.00  0 449 D
+ATOM    7560     C  CE1 ?  PHE    Dxp 174 ?   39.595   17.433   56.140   0.00  0 401 D
+ATOM    7638     O    O ?  LEU    Dxp 184 ?   33.870   17.251   55.188   0.00  0 411 D
+ATOM    7525     N  ND1 ?  HIS    Dxp 169 ?   36.365   20.155   60.429  -1.93  0 396 D
+ATOM    7558     C  CD1 ?  PHE    Dxp 174 ?   39.696   18.611   55.390   0.00  0 401 D
+ATOM    7524     C   CG ?  HIS    Dxp 169 ?   36.743   21.442   60.097   0.00  0 396 D
+ATOM    7527     C  CE1 ?  HIS    Dxp 169 ?   35.170   20.180   60.996   0.00  0 396 D
+ATOM    7528     N  NE2 ?  HIS    Dxp 169 ?   34.778   21.438   61.089   0.00  0 396 D
+ATOM    7526     C  CD2 ?  HIS    Dxp 169 ?   35.750   22.249   60.547   0.00  0 396 D
+ATOM    7637     C    C ?  LEU    Dxp 184 ?   33.727   17.072   53.991   0.00  0 411 D
+ATOM    7523     C   CB ?  HIS    Dxp 169 ?   38.074   21.770   59.468   0.00  0 396 D
+ATOM    7556     C   CB ?  PHE    Dxp 174 ?   40.965   20.182   53.857   0.00  0 401 D
+ATOM    7513     C  CG2 ?  THR    Dxp 167 ?   39.795   26.405   56.782   0.00  0 394 D
+ATOM    7510     O    O ?  THR    Dxp 167 ?   41.927   23.289   56.784   0.00  0 394 D
+ATOM    7517     O    O ?  ALA    Dxp 168 ?   40.187   24.764   60.121  -3.35  0 395 D
 # 
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Peter Schmidtke	251065b939	Merge pull request #147 from pegerto/m1_modfile compile M1/M2 chip molfile plugin	2024-07-23 10:24:59 +02:00
Pegerto Fernandez	4f54a742c2	small readme commit	2024-06-13 10:00:23 +01:00
Pegerto Fernandez	6c5db32fdd	compile M1/M2 chip molfile fork	2024-06-13 09:53:20 +01:00
Peter Schmidtke	9f2f379997	Merge pull request #144 from Discngine/ms-4.2 Bug fixes for 4.2 release	2024-04-08 12:08:48 +02:00
Peter Schmidtke	6e66d3677c	Added default dockerfile	2024-04-08 09:53:46 +00:00
Peter Schmidtke	146f76e8f8	Update readme	2024-04-08 09:52:17 +00:00
Peter Schmidtke	f792bff126	fixing MSE and Se issues	2024-04-08 09:42:28 +00:00
pschmidtke	d42000c72f	getting rid of hexnum writing for cif	2024-04-08 09:00:55 +02:00
Peter Schmidtke	a9eb68e8b9	Merge pull request #136 from Discngine/PeyratG-patch-1 fix coordinates writing in cif pockets	2024-03-20 11:07:09 +01:00
pschmidtke	16e7070daa	fixing reference test	2024-03-20 10:08:35 +01:00
PeyratG	b40990afb5	fix coordinates writing in cif pockets Issue observed while running fpocket on the PDB 7uit	2024-03-13 15:22:39 +01:00
Peter Schmidtke	2bfce34457	Merge pull request #133 from Discngine/issue-129 issue-129 correcting behaviour from pdb to mmcif	2024-02-23 21:33:54 +01:00
pschmidtke	6d7e84677b	issue-129 correcting behaviour from pdb to mmcif	2024-02-23 21:32:54 +01:00
Peter Schmidtke	1e861b184b	Merge pull request #132 from Discngine/issue-129 issue-129 adding insertion codes and splitting auth chain & residue n…	2024-02-16 20:46:16 +01:00
pschmidtke	4b3073e0de	adding missing reference updates	2024-02-16 20:40:26 +01:00
pschmidtke	675fe8c037	issue-129 adding insertion codes and splitting auth chain & residue numbers + longer filenames are supported now	2024-02-16 20:30:08 +01:00