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 <[email protected]> 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 <[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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