Turns out using non-adjacent numbers for the two domains works nicely. I
guess it's not too surprising that xplor wanted residue 1237 to be
connected to residue 1238.
On Thu, Jun 6, 2013 at 11:16 AM, Katherine Edmonds <kedmonds at bu.edu> wrote:
> 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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