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. :(
---------- Forwarded Message ----------
Subject: Re: [PyMOL] Fedora 3 problem
Date: Friday 22 April 2005 12:10 pm
From: Michelle Gill <michelle.gill@...>
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
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
Keep me posted on this!
New Haven, CT
> From: Gareth Stockwell <gareth@...>
> To: pymol-users <pymol-users@...>
> 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.