[PyMOL] Object-specific transparency
I would like to make one isosurface transparent, and leave another solid (or set different levels of transparency for each). I know object-specific transparency works for molecule objects, e.g. load molA.pdb, A load molB.pdb, B show surface, A show surface, B set transparency, 0.5, A (object B remains solidly-rendered) But if I try the same for isosurfaces, e.g. load mapA.ccp4, mapA load mapB.ccp4, mapB isosurface surfA, A, 1 isosurface surfB, B, 1 set transparency, 0.5, surfA ...the transparency of BOTH isosurfaces changes, as reflected by the messages in the console: PyMOLset transparency, 0.5, surfA Setting: transparency set to 0.5 in object 'mapA'. Setting: transparency set to 0.5 in object 'mapB'. Setting: transparency set to 0.5 in object 'surfA'. Setting: transparency set to 0.5 in object 'surfB'. Is there a way to make isosurface objects behave in the same way as the molecule objects? Gareth -- - Gareth Stockwell PhD student, Thornton Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548Personal homepage: http://www.ebi.ac.uk/~gareth
Re: [PyMOL] Suppress some output
Is there a way to keep my program 'quiet', or I can customize the output message myself? Depending on your OS and shell, something like this may work: denethor:~ /usr/local/pymol/pymol.com /dev/null 2/dev/null This works under Bash in any modern Linux distribution, from what I've seen. I suspect it would work on Irix too (still using Bash). I've had the exact same problem- mainly with util.rainbow(). -Nat
[PyMOL] Re: fitting residues
Hello: I am trying to color residues off a cartoon loop and want to color the sticks version of the residue down to the Ca, but not the Ca itself (ie. the residue and the cartoon are different colors). The problem is that if I color the Ca, then that section of the cartoon also gets colored. If I don't color the Ca, then the cartoon loop color comes halfway up the bond to the Cbeta. Does anybody have any suggestions, that is if I haven't made the question so convoluted you can understand it. Thanks in advance. Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
