Frieda wrote: > Can someone tell me whether altLoc or some other means of dealing > with alternate conformations of residues was implemented in Jmol, and > if so, point me to some documentation/discussion on exactly how to > use it?
No, this was not implemented. > There are a couple of threads on the Jmol email lists > involving the complications of dealing with alternate conformations, > but I can't seem to find a resolution to the discussion, if there was > one. I was unable to come up with a solution that I thought was tractable. I became depressed when I learned that each 'run' of alternate conformations was completely independent. Assume that there are two independent runs of alternate conformations. The first has m alternate conformations ... the second has n alternate conformations. Then there are m*n possible 'models' that could be generated. In the general case there can be 'r' independent runs. Therefore, we cannot statically generate all of the models. I think that we would need additions to the scripting language in order to allow one to choose which alternate conformation was/is desired out of each run. There needs to be a way to 'name' each of these different models. >From my perspective, support for alternate conformations is on hold until someone steps forward with a concrete proposal on how it should be implemented. Jan is very interested in this subject and has made some recommendations, but I was unable to follow his descriptions/recommendations and visualize how it could be implemented. Miguel ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid0709&bid&3057&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
