My software notes

February 3, 2006

making dimer PSF

Filed under: xplor/xplor-nih/cns — kpwu @ 10:34 pm

got from xplor-NIH discussion mailing list.

two ways to generate dimer PSF:

  1. If you have a PSF file for the monomer, it’s easy to create one for
    the dimer using the “classic”
    xplor interface. Try this:
    struct @monomer.psf end
    vector do (segid = “A”) (all)
    struct @monomer.psf end
    vector do (segid = “B”) (not segid A)
    write struct output = “dimer.psf” end
    stop
    (by JK)
  2. In the Python interface, easiest is:
    seq=”’ string containing three character residue names”’import psfGen
    psfGen.seqToPSF(seq,segName=’A’)
    psfGen.seqToPSF(seq,segName=’B’)

    #if you wish to save psf info:
    xplor.command(“write psf output=new.psf end”)
    (by CS)

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