[PyMOL] assigning atom types

Hi, I need to assign atom types for glycans and organic molecules. I can't relly on the atom types in the pdb, since in general there is not atom type information (e.g. all carbons are equal). Does PyMOL offers some feature to make this assignment easier? like checking the hybridization and valen

[PyMOL] get_sasa atom vs hetatm

Hi, I have noticed that computing the SASA using the PyMOL function "get_area" returns a reasonable value if the PDB has the record "ATOM" and a larger value (about 1 order of magnitude larger) if the record is "HETATM". Is this a bug, or some intended feature? Other people in my group were able t

Re: [PyMOL] Logging commands errors

Hi Matt, this is fixed in 1.7.6 (or since SVN rev 4109). Cheers, Thomas On 13 May 2015, at 12:05, Matthew Baumgartner wrote: > Hi, > I'm using pymol 1.7.4 from the SVN. When I use the File > Log... feature > to log the commands that I use to a file the output commands are not > recognized

[PyMOL] Logging commands errors

Hi, I'm using pymol 1.7.4 from the SVN. When I use the File > Log... feature to log the commands that I use to a file the output commands are not recognized when I do File > Run... in a new session. To reproduce: Open a new pymol session. File > Log... "log.pml" Change the background to white.