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2014-03-28T02:16:24Z

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Speleo3: 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

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..."

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'''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.

Similar functionality is also provided by the graphical [[Builder]] in "Protein" mode.

''New in PyMOL version 1.2''

== USAGE ==

fab input [, name [, mode [, resi [, chain [, segi [, state [, dir [, hydro [, ss [, async ]]]]]]]]]]

== ARGUMENTS ==

* input = string: Amino acid sequence in one-letter code

* name = string: name of object to create or modify {default: obj??}

* mode = string: Only supported mode is "peptide" {default: peptide}

* resi = integer: Residue number to start numbering from {default: 1}

* chain, segi = string: Chain id and segment id to assign

* state = integer: {default: -1}

* dir = 0/1: 0=append to N-terminus, 1=append to C-terminus {default: 1}

* hydro = 0/1: With or without hydrogens (BROKEN! Use [[Settings|auto_remove_hydrogens]]}

* ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat {default: 0}

== EXAMPLE ==

The two examples produce the same result:

<source lang="python">
# use resi and chain attributes
fab KVRISAEL, myprot1, resi=10, chain=B, ss=2

# use advanced syntax
fab B/10/ KVRISAEL, myprot2, ss=2
</source>

== SEE ALSO ==

* [[Builder]]
* [[Peptide Sequence]]
* [[CreateSecondaryStructure]]
* [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#model build_seq.py] by Robert Campbell

[[Category:Commands]]
[[Category:Editing Module]]

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