Thanks for the suggestion; this looks promising. What do I need to do to
force it to regard residues 1022:1237 as a separate protein from residues
1238:1428? I was reluctant to try to use chain identifiers to force them to
be separate, since I've had problems using chain identifiers in xplor in
the past, but is that what I need to do?
By the way, are the resid ranges treated as inclusive, so that 'resid 1:3'
means 'resid 1 or resid 2 or resid 3', or is it more like a python slice,
where it would mean 'resid 1 or resid 2'?
Thanks,
Katie
On Wed, Jun 5, 2013 at 9:22 PM, Charles Schwieters
<charles at schwieters.org>wrote:
>
> Hello Katie--
>
> >
> > I have a model of a protein-protein complex, where several residues in a
> loop
> > in the interface are undefined. I want to use xplor to add the loop
> residues,
> > and put them in a location that does not clash with the rest of the
> protein
> > or with the binding partner.
> >
> > I used addAtoms2.py to generate the loop residues without disturbing the
> rest
> > of the structure. The loop that was generated clashed with the binding
> > partner, so I wanted to run some dynamics to move the loop into a more
> > suitable position, again without disturbing the rest of the model.
>
> This is reasonable, and the overlap is pretty much to be expected.
>
> >
> > I found the dock.py script has some features to treat the proteins
> > as rigid bodies, and to prevent sidechain movement, while allowing
> > some movement in a defined part of the protein(s). So I'm trying to
> > use the dock.py script, with
>
> That script is a bit more complicated than you need. You might instead
> work from gb1_rdc/refine.py and disable (comment-out) all the
> experimental terms. Then, replace the line
>
> protocol.torsionTopology(dyn)
>
> with
>
> dyn.fix("resid 1022:1237")
> dyn.fix("resid 1238:1329")
> dyn.fix("resid 1338:1428" )
> protocol.cartesianTopology(dyn)
>
> and
>
> protocol.cartesianTopology(minc)
>
> with
>
> minc.fix("resid 1022:1237")
> minc.fix("resid 1238:1329")
> minc.fix("resid 1338:1428" )
> protocol.cartesianTopology(minc)
>
> I'm assuming that these selections are the regions which should not
> move at all.
>
> I do hope this helps--
> Charles
>
> --
> Charles Schwieters email: Charles at Schwieters.org
> www: http://schwieters.org/cds
> phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
>
>
>
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