[PyMOL] xquartz flicker with pymol

Dear all, after upgrading xquartz to the latest version (2.3.2, then 2.3.2.1), I am left with unusable pymol (installed via fink, pymol-py25 1.1r2-1001). When rotating objects the screen flickers like a disco strobe. Unfortunately, xquartz doesn't come with an obvious uninstaller. When I r

[PyMOL] selenomethionine

I am looking at a structure that contains selenomethionine (rendered MSE in the sequence). When I Show Surface, Se-Met is not displayed with a surface, but all the other residues are. Is there any way to make a surface over Se-Met as well? Scott --- Scott Le

Re: [PyMOL] selenomethionine

Scott, the MSEs are probably HETATM records instead of ATOM records. You can either replace the HETATM records to ATOM records or set surface_mode to 1 which allows rendering of surfaces with HETATM records (I think, am a bit fuzzy on that) HTH Carsten -Original Message- From

[PyMOL] Command line mode on OS X 10.4 vs 10.5

Howdy, Under OS X 10.4, I can do this: [b...@flange][/nfs/home/bene] /programs/i386-mac/pymol/1.1r1/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL -qc [b...@flange][/nfs/home/bene] echo $? 0 But on 10.5, I get this: [b...@macintel27][/nfs/home/bene] /programs/i386-mac/pymol/1.1r1/PyMOLX11Hybrid.