[phenixbb] rosetta fragment files -- adjusting residue numbers to combine them

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jun 16 12:24:55 PDT 2011

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
fragments_adjusted <start_resno>"

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[1]=" %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

>> [phenixbb-bounces at phenix-online.org] On Behalf Of Leonid Sazanov
[sazanov at mrc-mbu.cam.ac.uk]
>> Sent: 16 June 2011 13:11
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] rosetta fragment files
>> Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta
3.2.1. All rosetta tests passed OK.
>> I have several large protein chains in the starting model (already
>> So I had to get several pairs of fragment files from robetta server and
list all of them in the script.
>> Then mr_rosetta fails at the REBUILD_1 stage with the message:
>> could not open file (fragment file), although file is definitely there.
Is the reason that one can have only two input fragment files (3/9)?
Can several fragment files be combined into two 3/9 ones?
>> Thanks
>> --
>> Dr. Leonid A. Sazanov
>> Research group leader
>> Medical Research Council
>> Mitochondrial Biology Unit
>> Wellcome Trust / MRC Building
>> Hills Road
>> Cambridge
>> CB2 0XY
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