[phenixbb] rosetta fragment files

[Thomas C. Terwilliger]

Hi Leonid,

You're welcome!

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

fragment_files_chain_list
fragment_files_3_mer_by_chain
fragment_files_9_mer_by_chain

instead of fragment_files

starting with last night's build.
All the best,
Tom

>> Hi Tom,
>>
>> Thanks for that!
>> Native support for several large chains would be very useful.
>> Leonid
>>> 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:<50912.128.165.72.7.1308252295.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
>>> with:
>>>
>>>     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
>>> args=sys.argv[1:]
>>> if len(args) != 3:
>>>    print "USE: phenix.python adjust_robetta_resid.py  fragments_in
>>> fragments_adjusted<start_resno>"
>>>    sys.exit()
>>> file_in=args[0]
>>> file_out=args[1]
>>> start_resno=int(args[2])
>>>
>>> print "Copying %s to %s offsetting start residue number to %d" %(
>>>     file_in,file_out,start_resno)
>>>
>>> f=open(file_out,'w')
>>> new_resno=0
>>> for line in open(file_in).readlines():
>>>    if line.find('position:')>  -1 and line.find('neighbors:')>-1:
>>>       spl=line.split()
>>>       current_resno=int(spl[1])
>>>       new_resno=current_resno+start_resno
>>>       print "Residue %d changed to %d" %(current_resno,new_resno)
>>>       spl[1]=" %d " %(new_resno)
>>>       new_line="  ".join(spl)
>>>    else:
>>>       new_line=line
>>>    print>>f, new_line.rstrip()
>>>
>>> f.close()
>>> --------------------------------
>>>
>>> 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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