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[[email protected]] On Behalf Of Leonid Sazanov [[email protected]] Sent: 16 June 2011 13:11 To: [email protected] 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
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
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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