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Hello Ben--
>
> I'd like to use pdb2psf to generate a psf file for a protein with
> nonconsecutive numbering, but currently psfgen breaks the chain where the
> residue numbers are not consecutive:
>
> if seq:
> if (seg!=curSeg or
> resid!=curResid and resid!=curResid+1):
> #print "seq change termination >%s< >%s<" % ( seg,
> curSeg)
> terminate=1
> lostRes=res
>
> If I comment out the terminate then the numbering continues from the start
> residue.
>
The simplest fix for this case is to create a customized version of
pdb2psf. Before the final line of the script, place something like this:
gapSize=24
for atom in AtomSel("resid 30:41"):
atom.setResidueNum( atom.residueNum()+gapSize )
where you must specify gapSize and the residue range in the atom
selection.
hope this helps--
Charles
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