Re: [PyMOL] Superimpose small non-protein molecules?

Looks like PymolWiki is down. On Tue, May 5, 2015 at 1:59 PM, Osvaldo Martin wrote: > Hi Jorge, > > You are right align is only for proteins. You can use the Fit > command > > Cheers, > Osvaldo. > > On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossi

[PyMOL] Difficulty with Pymol segfault in CentOS 7 VM

Hello, I have recently installed Pymol 1.7.6 (also tested with 1.7.4 and 1.6.0) using gcc 4.8.3-9 on CentOS 7. The operating system is installed in VMware workstation 10.0.5 with hardware acceleration enabled. I installed the scripts and modules in an independent directory as described here: http:

Re: [PyMOL] Load very similar molecules into distinct objects?

Hi Jorge - As long as the filenames are different, the molecules should end up in separate objects. If the filenames are in fact the same (e.g. same filename but in different folders), try explicitly naming the objects using the PyMOL command line: load path/to/the/first/mol1.pdb, first_mol lo

Re: [PyMOL] Superimpose small non-protein molecules?

Hi Jorge, You are right align is only for proteins. You can use the Fit command Cheers, Osvaldo. On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: How can I superimpose two small non-protein molecules in PyMol? I

[PyMOL] Superimpose small non-protein molecules?

How can I superimpose two small non-protein molecules in PyMol? I think that "align" is not working because it assumes that the molecules are proteins and contain residues. --- [http://5.cim.co.cu/cim.gif] -

[PyMOL] Load very similar molecules into distinct objects?

When I load two molecules into pymol which are very similar, they automatically get clumped into the same object as different states. How can I circumvent this behavior? I want to load two molecules which are very similar into different objects. I know about the "split_states" command, but I am