Fwd: Re: [PyMOL] Fedora 3 problem, part 2

[Michelle G. <mic...@ya...>]

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 <mic...@ya...>
To: pym...@li...

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 <ga...@eb...>
> To: pymol-users <pym...@li...>
> 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

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