chore: commit empty .env

.env

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+# USAGE INSTRUCTIONS:
+# - copy this file and rename it to `.env` to use it.
+# - do not commit the `.env` file to version control. 
+# - you will need to set the paths below as appropriate for your environment.
+#   We provide examples in the comments to give you an idea of the expected format.
+
+
+# --- Mirrors to RCSB data ---
+# The `PDB_MIRROR_PATH` is a path to a local mirror of the PDB database. It's 
+# expected that you use the same saving conventions as the RCSB PDB, which means:
+#   `1a2b` --> /path/to/pdb_mirror/a2/1a2b.cif.gz
+# To set up a mirror, you can use tha atomworks commandline: `atomworks pdb sync /path/to/mirror`
+PDB_MIRROR_PATH=
+
+# The `CCD_MIRROR_PATH` is a path to a local mirror of the CCD database.
+# It's expected that you use the same saving conventions as the RCSB CCD, which means:
+#  `HEM` --> /path/to/ccd_mirror/H/HEM/HEM.cif
+# To set up a mirror, you can use the atomworks commandline: `atomworks ccd sync /path/to/mirror`
+# If no mirror is provided, the internal biotite CCD will be used as a fallback. To provide a 
+# custom CCD for a ligand, you can place it in the in the CCD mirror path following the CCDs pattern.
+# Example: /path/to/ccd_mirror/M/MYLIGAND1/MYLIGAND1.cif
+CCD_MIRROR_PATH=
+
+
+# --- External tools ---
+# The `X3DNA_PATH` is a path to the x3dna tool, which is used for DNA structure analysis.
+# Example: /path/to/x3dna-v2.4
+X3DNA_PATH=