Fab

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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}
  • 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