[PyMOL] gradient transparency

Any ideas? Cheers, Neil. ***** Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, Institute of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT. UK. Tel: +44 (0) 113 343 7065 Fax: +4

[PyMOL] Suse 10 and PyMOL crashes

I'd see if anyone else had had similar experiences so far. Everything else about the machine is rock-solid and stable, including the latest build of Chimera that is running exceptionally well. Best regards, Neil Ranson

Re: [PyMOL] Suse 10 and PyMOL crashes

Thanks for the reply. "Irretrievably crashing" means that everything stops dead. The screen freezes, mouse/keyboard become unresponsive, the machine becomes unreachable (via ssh or even ping) from other workstations. Background processes instantaneously halt. A 'proper' crash in other words!

[PyMOL] PyMOL and Suse10.0

even recent beta drivers to the best of my knowledge. Neil Ranson -- N.A.Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. n.a.ran...@leeds.ac.uk

[PyMOL] Capping cut surface of map

ion, which I would dearly like to recreate in a pymol script. Any thoughts, suggestions (or promises of new features in upcoming versions!) would be much appreciated. Cheers, Neil. Neil Ranson PhD email: n.a.ran...@leeds.ac.uk

[PyMOL] label transparency

Dear All, Does anyone now if it's possible to alter the transparency level of a label? I have an object that is scripted to fade in and out, and I would like to bring the labels in and out at the same speed, but can't seem to find a setting that works. Thanks in advance, Ne

[PyMOL] Different colours for inner and outer surface.

outside surfaces, similarly coloured. Thanks in advance, Neil * Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, School of Biochemistry & Microbiology, University of Leeds, Leeds, LS2 9JT. UK. n.a

[PyMOL] multi cpu rendering

Dear All, I've been preparing figures for a manuscript on a Sun v40z with 4 x Opteron 850 cpu's and 8Gb of memory (and Suse9.0). When I start pymol: > pymol.com -c script.pml pymol says that it detects 4cpu and enables multithreaded rendering, but I never see it u

[PyMOL] RE: multi cpu rendering

Dear All, Thanks for public and private replies alike. The "set max_threads, n" construct works a treat, giving a 3.6x speedup going from 1 to 4 cpu's. A quad opteron is now an extremely fast rendering machine indeed! Best regards, Neil.

[PyMOL] removing loops

g artefacts in the image. Any help would be much appreciated. Cheers, Neil. ***** Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, School of Biochemistry & Microbiology, University of Leeds, Leeds, LS2 9JT.

[PyMOL] camera and clipping planes

t; of that cut map (which can't think how to do at all!). Maybe there's a fiendishly clever way..? Cheers Neil. ********* Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, School of Biochemistry & Micr

[PyMOL] RE: hardware stereo - monitors

Hi there, Try an iiyama HM204DTA (at least in the UK) which will do >100Hz up to 1600x1200. I have one and at 1280x1024 @ 120Hz it works beautifully for me. Regards, Neil. ***** Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecu