Hi Andrew, I have tried similar things in the past. Perhaps I am old fashioned, but I am still using xplor (the old syntax). Anyway, with this xplor I noticed that fixing does work:
constraint fix=(select ##) end Grouping is only allowed in torsion angle dynamics and rigid body dynamics. But it could be that this has improved in (py)Xplor-NIH. It took me quite some time to find this out, since Xplor litterature and documentation is not known to be easily accessible. [For this reason I stick to "the old xplor", since I know the syntax and by now I know ?(better) what happens] Regards, Ramon Radboud University Nijmegen Dept. Biophysical Chemistry > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. Fix and group (Andrew Severin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Jan 2009 08:45:34 -0600 > From: "Andrew Severin" <severin at iastate.edu> > Subject: [Xplor-nih] Fix and group > To: xplor-nih at nmr.cit.nih.gov > Message-ID: > <544b4b9a0901140645o4143dd0cu4a13774cc0f39b68 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone, > > I am trying to create a model of a two domain protein that oligomerizes. > I have the structure of the single domain interaction (A binding B). > Think of it as domain orientation of a dual domain protein that also > dimerizes. > > I would like to fix this structure and allow the adjacent domains to > minimize around this structure based on RDC and or NOEs. > > I tried to fix the domains in the interaction as seen below. I put these > lines in the same part of the refine.py that was suggested and worked for > domain orientation. The problem is that the domains don't stay fixed at > the > dimer interface. > > bbStr = "(name N or name C or name CA or name O or name H or name HA)" > sh2Sel = select('resid 233:339') > sh2SideChainSel = select("not " + bbStr + " and resid 233:339") > sh3Sel= select('resid 173:229') > sh3SideChainSel = select("not " + bbStr + " and resid 173:229") > sh2aSel = select('resid 1233:1339') > sh2aSideChainSel = select("not " + bbStr + " and resid 1233:1339") > sh3aSel= select('resid 1173:1229') > sh3aSideChainSel = select("not " + bbStr + " and resid 1173:1229") > > > fullgroupListsh3= [] > fullgroupListsh2=[] > fullgroupListsh3.append( selLogic("sh2Sel and not sh2SideChainSel",vars()) > ) > fullgroupListsh3.append( selLogic("sh3Sel and not sh3SideChainSel",vars()) > ) > fullgroupListsh3.append( selLogic("sh2aSel and not > sh2aSideChainSel",vars()) > ) > fullgroupListsh3.append( selLogic("sh3aSel and not > sh3aSideChainSel",vars()) > ) > > dyn.fix(select('resid 1233:1339 and resi 173:229')) > dyn.setGroupList( fullgroupListsh3 ) > > Thanks, > > Andrew Severin > Iowa State University > PhD May 2009 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090114/a66f1066/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 71, Issue 3 > **************************************** >
