Usage
Usage: cath-refine-align alignment_source protein_file_source [superposition_outputs]
Iteratively refine an existing alignment by attempting to optimise SSAP score
Please specify:
* at most one alignment (default: --do-the-ssaps)
* one method of reading proteins (number of proteins currently restricted to 2)
PyMOL is started if no alignment or superposition output option is specified
Miscellaneous:
-h [ --help ] Output help message
-v [ --version ] Output version information
[1mInput[0m:
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> (=HEAVY) 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
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"))
[1mOutput[0m:
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)
Please tell us your cath-tools bugs/suggestions : https://github.com/UCLOrengoGroup/cath-tools/issues/new
