Fab

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 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:

# use resi and chain attributes
fab KVRISAEL, myprot1, resi=10, chain=B, ss=2

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

SEE ALSO

• Builder
• Peptide Sequence
• CreateSecondaryStructure
• build_seq.py by Robert Campbell