https://pymolwiki.org/index.php?title=Fab&feed=atom&action=historyFab - Revision history2024-03-29T00:54:20ZRevision history for this page on the wikiMediaWiki 1.35.7https://pymolwiki.org/index.php?title=Fab&diff=9213&oldid=prevSpeleo3: Created page with "'''fab''' builds peptide entities from sequence. The sequence must be specified in one-letter code. Several fragments will be created if the sequence contains spaces (chain break..."2011-08-03T16:58:55Z<p>Created page with "'''fab''' builds peptide entities from sequence. The sequence must be specified in one-letter code. Several fragments will be created if the sequence contains spaces (chain break..."</p>
<p><b>New page</b></p><div>'''fab''' builds peptide entities from sequence. The sequence must be specified in one-letter code. Several fragments will be created if the sequence contains spaces (chain breaks). To specify chain-id and residue number, an advanced syntax pattern like ''chain/resi/'' can be put before each sequence fragment.<br />
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Similar functionality is also provided by the graphical [[Builder]] in "Protein" mode.<br />
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''New in PyMOL version 1.2''<br />
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== USAGE ==<br />
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fab input [, name [, mode [, resi [, chain [, segi [, state [, dir [, hydro [, ss [, async ]]]]]]]]]]<br />
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== ARGUMENTS ==<br />
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* input = string: Amino acid sequence in one-letter code<br />
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* name = string: name of object to create or modify {default: obj??}<br />
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* mode = string: Only supported mode is "peptide" {default: peptide}<br />
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* resi = integer: Residue number to start numbering from {default: 1}<br />
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* chain, segi = string: Chain id and segment id to assign<br />
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* state = integer: {default: -1}<br />
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* dir = 0/1: 0=append to N-terminus, 1=append to C-terminus {default: 1}<br />
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* hydro = 0/1: With or without hydrogens (BROKEN! Use [[Settings|auto_remove_hydrogens]]}<br />
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* ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat {default: 0}<br />
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== EXAMPLE ==<br />
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The two examples produce the same result:<br />
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<source lang="python"><br />
# use resi and chain attributes<br />
fab KVRISAEL, myprot1, resi=10, chain=B, ss=2<br />
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# use advanced syntax<br />
fab B/10/ KVRISAEL, myprot2, ss=2<br />
</source><br />
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== SEE ALSO ==<br />
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* [[Builder]]<br />
* [[Peptide Sequence]]<br />
* [[CreateSecondaryStructure]]<br />
* [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#model build_seq.py] by Robert Campbell<br />
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[[Category:Commands]]<br />
[[Category:Editing Module]]</div>Speleo3