Hi Charles We also thought that the center averaging would work. In the calculations we do, however, get two distinct orientations of the first Trp, one where HE3 is close to CE2 of the second Trp and one where it is close to CZ3.
>From browsing the old Xplor manual the SUM averaging is apparently forced when using OR in the atom selection. I guess the center averaging only works when you select several atom using a wild-card. See: http://nmr.cit.nih.gov/xplor-nih/xplorMan/node380.html#noe-ambiguity The way we set up the noe term was the following: for (name,scale,aveType,file) in [('all',1,'sum',"nonredun_20110929.tbl"), ('cs',1,'center',"ambig.tbl") ]: pot = create_NOEPot(name,file) pot.setScale(scale) pot.setAveType(aveType) noe.append(pot) where the HE3 to CE2/CZ3 restraint is in the ?cs? list. Cheers, Kaare On 11/2/11 2:46 PM, "Charles Schwieters" <charles at schwieters.org> wrote: > > Hello Kaare-- > >> >> I have a question concerning an atom selection in a special case. I need to >> make a restraint between a proton and the exact center of an aromatic ring >> (in this case the 6-ring in a tryptophan indole). So far, I've tried to >> define it as an NOE in the following way: >> >> ASSIGN (RESID 19 AND NAME HE3) ( (RESID 20 AND NAME CE2) or (RESID 20 AND >> NAME CZ3) ) 2.5 1.0 1.0 >> >> and setting avetype to SUM for this restraint. It was evident, that the 19 >> HE3 either was restrained to CE2 OR CZ3 and not in between them. How should I >> write the NOE in order to select the center of the tryptophan ring - is this >> possible? >> > > As Keith wrote, Center averaging should do what you want, either in > the Python or old XPLOR interface. Perhaps there's a problem with the > syntax? Brief examples of setting up the noe term can be found in > python/tests/noeTest*.py > and in > test/noetest*.inp > > If you can find a case where the distance is definitely not between > the atom in the first selection and the center position of the atoms > in the second, it is a bug, and I'd like to know about it. > > best regards-- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20111102/cb166f00/attachment-0001.html
