cath-superpose.ubuntu-20.04

Description

============
cath-superpose v0.16.10-0-g99edb28 [2021-04-20]
============

Superpose protein structures using an existing alignment

Build
-----
   Apr 20 2021 13:24:46
   GNU C++ version 10.2.0
   GNU libstdc++ version 20200808
   Boost 1_71

Usage

Usage: cath-superpose alignment_source pdb_file_source [superposition_outputs]

Superpose protein structures using an existing alignment

Please specify:
 * at most one superposition JSON or alignment (default: --do-the-ssaps)
 * one method of reading PDB files (number to match the alignment)

PyMOL is started if no alignment or superposition output option is specified

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

Input:

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>              Glue pairwise alignments together using SSAP scores in file <file>
                                           Assumes all .list alignment files in same directory
  --do-the-ssaps [=<dir>(="")]             Do the required SSAPs in directory <dir>; use results as with --ssap-scores-infile
                                           Use a suitable temp directory if none is specified

Alignment refining:
  --align-refining <refn> (=NO)            Apply <refn> refining to the alignment, one of available values:
                                              NO    - Don't refine the alignment
                                              LIGHT - Refine any alignments with few entries; glue alignments one more entry at a time
                                              HEAVY - Perform heavy (slow) refining on the alignment, including when gluing alignments together
                                           This can change the method of gluing alignments under --ssap-scores-infile and --do-the-ssaps

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   ")

Regions:
  --align-regions <regions>                Handle region(s) <regions> as the alignment part of the structure.
                                           May be specified multiple times, in correspondence with the structures.
                                           Format is: D[5inwB02]251-348:B,408-416A:B
                                           (Put <regions> in quotes to prevent the square brackets confusing your shell ("No match"))

Output:

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)

Superposition content:
  --regions-context <context> (=alone)     Show the alignment regions in the context <context>, one of available options:
                                              alone    - alone
                                              in_chain - within the chain(s) in which the regions appear
                                              in_pdb   - within the PDB in which the regions appear
  --show-dna-within-dist <dist> (=4)       Show DNA within <dist>Å of the alignment regions
  --show-organic-within-dist <dist> (=10)  Show organic molecules within <dist>Å of the alignment regions

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