cath-superpose

Description

============
cath-superpose v0.14.1-0-gbb6e6a3 [2017-05-31]
============

Superpose protein structures using an existing alignment

Build
-----
   May 31 2017 08:33:21
   Clang version 3.6.2 (branches/release_36)
   GNU libstdc++ version 20160726
   Boost 1_57

Usage

Usage: cath-superpose alignment_source pdb_file_source [superposition_outputs]

Superpose protein structures using an existing alignment

Please specify:
 * one superposition JSON or alignment
 * one method of reading PDB files (number to match the alignment)

Miscellaneous:
  -h [ --help ]                   Output help message
  -v [ --version ]                Output version information

Alignment source:
  --res-name-align                Align residues by simply matching their names (numbers+insert)
                                  (for multiple models of the same structure)
  --fasta-aln-infile <file>       Read FASTA alignment from file <file>
  --ssap-aln-infile <file>        Read SSAP alignment from file <file>
  --cora-aln-infile <file>        Read CORA alignment from file <file>
  --ssap-scores-infile <file>     Read SSAP scores from file <file>
                                  Assumes all .list alignment files in same directory

Superposition source:
  --json-sup-infile <file>        Read superposition from file <file>

ID options:
  --id arg                        Structure ids

PDB files source:
  --pdb-infile <pdbfile>          Read PDB from file <pdbfile> (may be specified multiple times)
  --pdbs-from-stdin               Read PDBs from stdin (separated by line: "END   ")

Alignment output:
  --aln-to-cath-aln-file arg      [EXPERIMENTAL] Write the alignment to a CATH alignment file
  --aln-to-cath-aln-stdout        [EXPERIMENTAL] Print the alignment to stdout in CATH alignment format
  --aln-to-fasta-file arg         Write the alignment to a FASTA file
  --aln-to-fasta-stdout           Print the alignment to stdout in FASTA format
  --aln-to-ssap-file arg          Write the alignment to a SSAP file
  --aln-to-ssap-stdout            Print the alignment to stdout as SSAP
  --aln-to-html-file arg          Write the alignment to a HTML file
  --aln-to-html-stdout            Print the alignment to stdout as HTML

Superposition output:
  --sup-to-pdb-file arg           Write the superposed structures to a single PDB file arg, separated using faked chain codes
  --sup-to-pdb-files-dir arg      Write the superposed structures to separate PDB files in directory arg
  --sup-to-stdout                 Print the superposed structures to stdout, separated using faked chain codes
  --sup-to-pymol                  Start up PyMOL for viewing the superposition
  --pymol-program arg (="pymol")  Use arg as the PyMOL executable for viewing; may optionally include the full path
  --sup-to-pymol-file arg         Write the superposition to a PyMOL script arg
                                  (Recommended filename extension: .pml)
  --sup-to-json-file arg          Write the superposition to JSON superposition file
                                  (Recommended filename extension: .sup_json)

Viewer (eg PyMOL, Jmol etc) options:
  --viewer-colours <colrs>        Use <colrs> to colour successive entries in the viewer
                                  (format: colon-separated list of comma-separated triples of RGB values between 0 and 1)
                                  (will wrap-around when it runs out of colours)
  --gradient-colour-alignment     Colour the length of the alignment with a rainbow gradient (blue -> red)
  --show-scores-if-present        Show the alignment scores
                                  (use with gradient-colour-alignment)
  --scores-to-equivs              Show the alignment scores to equivalent positions, which increases relative scores where few entries are aligned
                                  (use with --gradient-colour-alignment and --show-scores-if-present)
  --normalise-scores              When showing scores, normalise them to the highest score in the alignment
                                  (use with --gradient-colour-alignment and --show-scores-if-present)

Usage examples:
 * cath-superpose --ssap-aln-infile 1cukA1bvsA.list --pdb-infile $PDBDIR/1cukA --pdb-infile $PDBDIR/1bvsA --sup-to-pymol
     (Superpose 1cukA and 1bvsA (in directory $PDBDIR) based on SSAP alignment file 1cukA1bvsA.list and then display in PyMOL)
 * cat pdb1 end_file pdb2 end_file pdb3 | cath-superpose --pdbs-from-stdin --sup-to-stdout --res-name-align
     (Superpose the structures from stdin based on matching residue names and then write them to stdout [common Genome3D use case])

Please tell us your cath-tools bugs/suggestions : https://github.com/UCLOrengoGroup/cath-tools/issues/new