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 <[email protected]>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: [email protected] > www: http://schwieters.org/cds > phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt > > >
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