Hi Peter, If you could send me the PDB (or one like it) I'd like to see it.
The known flags for controlling how PyMOL loads multi-state files are: discrete= 0 or 1 If 0, then all states must have the same number of atoms and similar connectivity If 1, then all states are treated as different molecular structures, so can have differing numbers of atoms and bonds multiplex= 0 or 1 If 0, then load the N-state file as one N-state object If 1, then load the N-state file as N one-state objects So, what happens in v1.3 if you write: load fileName.pdb, multiplex=0 Cheers, -- Jason On Wed, Mar 16, 2011 at 10:23 AM, <peter.st...@weizmann.ac.il> wrote: > Dear PyMol experts: > > When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has > 40 coordinate sets (each is one frame in an animation) each beginning > with: > HEADER Output iset= n "xxxx_G=r_0_01" > then a list of the pdb coordinates > and ending with: > ENDMDL > "n" ranges from 0 to 39. > This results in the following output: > HEADER Output iset= 0 "xxxx_G=r_0_01" > HEADER Output iset= 1 "xxxx_G=r_0_01" > ObjectMolReadPDBStr: read MODEL 1 > ObjectMolReadPDBStr: read MODEL 2 > etc. ... > ObjectMolReadPDBStr: read MODEL 39 > ObjectMolReadPDBStr: read MODEL 40 > CmdLoad: "/home/psstern/pymol/xxxx_G=r_0_01.pdb" loaded as "xxxx_G=r_0_01". > > This then displays one molecule with 40 frames and the animation can be > activated by clicking on the red arrow. > > However, when using Open-Source PyMOL 1.3 the same file results in > different behavior. Instead of reading in one object with 40 frames > it reads in 40 different objects and displays all of them. The output > I get is: > HEADER Output iset= 0 "xxxx_G=r_0_01" > HEADER Output iset= 1 "xxxx_G=r_0_01" > HEADER Output iset= 2 "xxxx_G=r_0_01" > etc. ... > HEADER Output iset= 38 "xxxx_G=r_0_01" > HEADER Output iset= 39 "xxxx_G=r_0_01" > CmdLoad: loaded 40 objects from "/home/psstern/pymol/xxxx_G=r_0_01.pdb". > > Is this a bug or am I missing some parameter which is set differently > by default for the two versions? I couldn't find a solution in the > on-line documentation. > > Regards, > Peter Stern > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
