[phenixbb] rosetta fragment files
Thomas C. Terwilliger
terwilliger at lanl.gov
Tue Jun 21 08:33:22 PDT 2011
I have now moved one step closer to what you really want. You can identify
which fragment files go with which chain using the keywords
instead of fragment_files
starting with last night's build.
All the best,
>> Hi Tom,
>> 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:<50922.214.171.124.7.1308252295.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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