[phenixbb] rosetta fragment files (Thomas C. Terwilliger)
sazanov at mrc-mbu.cam.ac.uk
Tue Jun 21 06:57:23 PDT 2011
Thanks for that!
Native support for several large chains would be very useful.
> Message: 3
> Date: Thu, 16 Jun 2011 13:24:55 -0600 (MDT)
> From: "Thomas C. Terwilliger"<terwilliger at lanl.gov>
> To: "PHENIX user mailing list"<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] rosetta fragment files -- adjusting residue
> numbers to combine them
> Message-ID:<509188.8.131.52.7.1308252295.squirrel at webmail.lanl.gov>
> Content-Type: text/plain;charset=iso-8859-1
> Hi Leonid and others wanting to use phenix.mr_rosetta with large chains,
> After looking at the Rosetta code and conferring with Frank DiMaio from
> the Baker laboratory...
> You can paste several fragment files together to represent your entire
> chain, but you need to edit all but the first one to set the position in
> the sequence file that each set of fragments goes with.
> Here is a little script that will take a fragments file that you have
> created that started with residue 651 and edit it in a way that you can
> just add to the end of your fragments file for residues 1-650. Run it
> phenix.python adjust_robetta_resid.py \
> fragments_in fragments_adjusted 651
> # adjust_robetta_resid.py
> # use: phenix.python adjust_robetta_resid.py fragments_in
> fragments_adjusted 651
> # to adjust the first residue of fragments_in to be 651
> import sys
> if len(args) != 3:
> print "USE: phenix.python adjust_robetta_resid.py fragments_in
> print "Copying %s to %s offsetting start residue number to %d" %(
> for line in open(file_in).readlines():
> if line.find('position:')> -1 and line.find('neighbors:')>-1:
> print "Residue %d changed to %d" %(current_resno,new_resno)
> spl=" %d " %(new_resno)
> new_line=" ".join(spl)
> print>>f, new_line.rstrip()
> I will add this to phenix as "phenix.adjust_robetta_resid" as well.
> However...there still is a problem if you have multiple chains...as
> mr_rosetta has only one set of fragments files the same fragments files
> are being applied to all your chains. I will add a way to specify which
> fragments files go with which chains.
> All the best,
> Tom T
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