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
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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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