Hi again, I just realized you were also having problems with dots, per the pictures on your website. I was unable to find a 'cure' for this. :(
Michelle Gill ---------- Forwarded Message ---------- Subject: Re: [PyMOL] Fedora 3 problem Date: Friday 22 April 2005 12:10 pm From: Michelle Gill <michelle.g...@yale.edu> To: pymol-users@lists.sourceforge.net Hi Gareth, I have experienced what I'm pretty sure is a similar problem on SuSE 9.2 Pro. I did not test this feature on my previous operating system (SuSE 9.1 Pro), so I can't, in my instance, say that it's operating system related. What operating system did you upgrade from? Fedora 3 and SuSE 9.2 both use X11.org instead of Xfree86, so I'm curious if the problem is related to this... I think Fedora 2 also used X11.org, although the problem could also be version specific. My hardware specs are posted at the end of this message. The good news is that I found a work-around for the three cases you mentioned. It seems to be related to the transparency setting. These are cartoon_transparency, sphere_transparency, and transparency for cartoons, spheres, and surfaces, respectively. Leaving them set to their defaults of 0 seems to cause the exact same problem you are having. I was able to get around this by setting them to some really small but non-zero number. The thresholds for each seem different. I can remedy the cartoon problem by setting cartoon_transparency=0.00001. This number is too small for spheres, though, and I must set sphere_transparency=0.0001 (note the order of magnitude difference). I didn't play around to find the exact threshold for each of these settings. IThe work-around for surfaces seems to be to set transparency=0.0001. There is no surface_transparency setting (that I can find). Setting transparency=0.0001 DOES NOT work for cartoons or spheres, though, so there must be something specific to surfaces about this command. Does anyone else have comments about this? PyMol gurus? Warren? I also have Widows XP on this computer but have not tested the above issue. I will try to do so sometime in the near future. My hardware/OS specifications: HP Pavilion Laptop zv5445 Pentium 4, 3.2 GHz HT 500 MB RAM 100 GB Hard drive 1280 x 800 Brightview screen ATI Radeon Mobility 9000 IGP (no 3D acceleration running though) 128 MB video RAM SuSE 9.2 Pro Kernel 2.6.8-24.13-smp i686 X11.org 6.8.1 Windows XP Keep me posted on this! Michelle Gill Graduate Student Yale University New Haven, CT > From: Gareth Stockwell <gar...@ebi.ac.uk> > To: pymol-users <pymol-users@lists.sourceforge.net> > Organization: European Bioinformatics Institute > Date: 21 Apr 2005 20:10:08 +0100 > Subject: [PyMOL] Fedora 3 problem > > > I recently upgraded to Fedora Core 3 and have been having some strange > problems with PyMOL. > > Molecules look fine when rendered as lines, sticks or mesh, but spheres, > surfaces, and sometimes cartoons only appear for half the molecule. See > the following page for examples of this. I've also posted various > diagnostic information in the hope that some Linux guru out there may be > able to help. > > The graphics card is an Intel 82865G. This is (in theory) supported > out-of-the box by FC3; I have not installed anything except the > distribution. The Intel homepage has some drivers for this card, but > they are the same as the ones bundled with FC3. When I tried installing > them after the OS, I got exactly the same problem. > > http://www.ebi.ac.uk/~gareth/pymol/fc3_problem > > Gareth -------------------------------------------------------
