> Miguel, > >> Q: Are these distinct atoms in the same 'model' or in >> different 'models' ? > > They are real and distinct atoms in the same model, which is a big > downside of PyMOL's approach.
OK > count_atoms, for instance, will be > increased...even though that isn't right from a conceptual standpoint. Of > course, the atom count could probably be weighted by the occupancies, and > in theory occupancies should sum to 1.0, but...well, you get the idea -- > it is a bit of a mess. Understood. Some time ago I did some prototyping where I put all of the altLoc atoms in the same model. One of the first things that I saw was that the 'autobond' code that builds connectivity just fell apart. Places where there altLoc atoms just turned into a knot of spaghetti. This is one of the things that made me think that it was necessary to build separate models. But, the number of distinct models quickly gets too large. 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
