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110 lines
3.5 KiB
Markdown
110 lines
3.5 KiB
Markdown
# NAME
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mkdssp - Assign secondary structure to proteins
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# SYNOPSIS
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mkdssp \[OPTION\] input \[output\]
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# DESCRIPTION
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The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
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standardize secondary structure assignment. DSSP is a database of
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secondary structure assignments (and much more) for all protein entries
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in the Protein Data Bank (PDB). mkdssp is the program that calculates
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DSSP entries from PDB entries. mkdssp does **not** predict secondary
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structure.
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The original DSSP program wrote output in a fixed format, this version
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by default writes annotated mmCIF files, storing the secondary structure
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information in the \_struct_conf category.
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Since version 4.0 the mkdssp program also assigns PPII helices.
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# OPTIONS
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The input file can be either mmCIF or PDB format and the file may be
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gzip compressed. Note that input files must be formatted correctly. E.g.
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PDB files must have a CRYST1 record. More info:
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https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1
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The output is optional, if omitted the output is written to *stdout*. If
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the name of the output file ends with either *.gz* or *.bz2* the output
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is compressed accordingly.
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**\--output-format**=\[dssp\|mmcif\]
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: If an output file is specified, the extension of the filename is
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used to choose to output format, but if it is unclear, mmcif is the
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default. Use this option to force output in either the old fixed
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column DSSP format or the new annotated mmCIF format.
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**\--no-dssp-categories**
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: When writing mmCIF files, suppress the output of all dssp\_
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categories.
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**\--min-pp-stretch**
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: This option can be used to define the minimal number of residues
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with PHI/PSI angles within the range required to assing a PP helix.
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**\--write-other**
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: By default the new format does not write the structure information
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for OTHER. Use this flag to change that.
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**\--components**
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: The knowledge of compounds is loaded from the CCD file
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*components.cif* that should have been installed by *libcifpp*. You
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can override that file by using this option.
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**\--extra-compounds**
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: As an addition to the standard *components.cif* file, you can add
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more files using this option. Files should be either in CCD format
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or should be CCP4 restraints files.
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**\--mmcif-dictionary**
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: The default mmCIF dictionary file is installed by the *libcifpp*
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library but you can override it using this option.
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# DETAILS
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The DSSP algorithm assings secondary structure based on the energy
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calculated for H-bonds.\
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**Table 1. Secondary Structures recognized**
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--------------- -------------- -------------
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DSSP Code mmCIF Code Description
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H HELX_RH_AL_P Alphahelix
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B STRN Betabridge
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E STRN Strand
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G HELX_RH_3T_P Helix_3
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I HELX_RH_PI_P Helix_5
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P HELX_LH_PP_P Helix_PPII
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T TURN_TY1_P Turn
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S BEND Bend
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' ' (space) OTHER Loop
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--------------- -------------- -------------
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# BUGS
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The mmCIF format currently lacks a lot of information that was available
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in the old format like information about the bridge pairs or the span of
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the various helices recognized. Also the accessibility information is
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left out.
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If you think this information should be part of the output, please
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contact the author.
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# AUTHOR
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Written by Maarten L. Hekkelman \<maarten@hekkelman.com\>
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# REPORTING BUGS
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Report bugs at https://github.com/PDB-REDO/dssp/issues
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