[phenixbb] rosetta fragment files (Thomas C. Terwilliger)

[Leonid Sazanov]

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
>