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. 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. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:[EMAIL PROTECTED] > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Miguel > Sent: Tuesday, May 09, 2006 7:01 PM > To: [email protected] > Subject: RE: [Jmol-users] update on altLoc or alternate conformation > > Warren wrote: > > Miguel, > > > > This is definitely one of the more un-dealt-with issues in > > macromolecular structure, and I don't know of any > satisfactory solution. > > Thanks for speaking up on this issue. > > > PyMOL's > > approach is to treat alternate conformations as distinct > atoms which > > share all identifiers except for the one-letter alt-conf > identifier, > > which is blank ('') for an atom which has no alternative > conformation. > > Thus, in PyMOL's atom selection language: > > > > an all A selection: alt ''+A > > an all B selection: alt ''+B > > or a specific mixed A/B selection: alt '' or (resi 120 & alt A) or > > (resi 130 & alt B) > > > > etc. > > OK > > You said that PyMOL treats them as distinct atoms ... > > Q: Are these distinct atoms in the same 'model' or in > different 'models' ? > > > Food for thought. Before choosing an implementation, I > suggest taking > > a look at how O, VMD, and DSViewer handle these as well. > > Excellent idea. Perhaps someone on the mailing list is > familiar with how some of these packages try to deal with the issues. > > > 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=k&kid0709&bid&3057&dat1642 > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------- 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
