Hello Jian-- Just getting back from vacation...
> Our current problem at hand is that we have resolved the structure > of a part of the protein (two helices), now we want to resolve the > full-length structure while keeping the resolved part intact. So is > it possible to do this, i.e., grouping the two helices as it is in > our resolved structure, while using xplor to calculate the structure > of the termini and loops that were not present previously. It seems > that during energy minimization, atoms can be grouped together, but > during simulated annealing using "AnnealIVM", can we do the > grouping? You can indeed use rigid body grouping using the ivm group method. For instance, if you have dyn=IVM() You can specify dyn.group( "resid X:Y" ) where X and Y are beginning and final residue numbers of a helix. Make certain that this grouping is performed before calling protocol.torsionTopology(dyn) Also, I suggest a subsequent refinement step in which the grouping is disabled- to get a better structure. best regards-- Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
