Hi All -
I am trying to compile the open-source code for PyMOL for the first time (on CentOS) and running into all sorts of issues.  Is there a listing somewhere of all the dependencies (and their versions) that I could use as a guide to get everything I need all at once, rather than continuing to fix compile failures one-at-a-time (which is confusing and frustrating)
Conversely, is there a distro that more-or-less "just works"?  I can create a virtual machine in which I compile, but I'm only allowed to have RHEL or CentOS on my physical machine...

From: Jason Vertrees [mailto:jason.vertrees@schrodinger.com]
Sent: Mon 2/13/2012 11:27 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Open Source PyMOL v1.5.0.1


It is my pleasure to announce the release of open source PyMOL
v1.5.0.1. The source code has been committed to the open-source
repository. It is revision 3976. An svn tag and downloadable bz2
source file were also created. All of this is accessible form the
PyMOL project page on SourceForge

Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
and AMD/ATI cards are known to work well. But, Intel Mobile and other
low-end cards might have issues with the new rendering. The majority
of rendering anomalies are fixed by simply upgrading your video

You should be able to pull and build just like normal. You will need Python 2.7.

Some simple testing on my Linux machine shows the following
improvements in real-time rendering performance for a large protein
(58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:

   240% increase (81 FPS to 270 FPS)
   864% increase (28 FPS to 270 FPS)
   2100% increase (8 FPS to 180 FPS)
   3757% increase (27 to 270 FPS)
   2600% increase (10 to 270 FPS)
   33% (180 FPS to 270 FPS)

Your numbers will be different. This Linux machine has a powerful card
used for development
It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
works for you it's because AMD/ATI helped out. You may want to thank
them. What I've seen is that the more powerful your card the greater
the _difference_ in speed. That is, low-end cards should see
improvements in the range of tens to hundreds of percent while more
powerful cards should register improvements like mine, in the
thousands of percent for some representations.

To quickly test performance of the new code on your machine just load
a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
rotate/translate it. To see the refresh rate, type "set
show_frame_rate". The refresh rate shows up in the lower right hand
corner. Compare the frame rate, smoothness, and rendering quality when
the setting "use_shaders" is turned off and when it's turned on.
Compare different representations, each time turning on and off the
"use_shaders" setting.

You can quickly update old PyMOL session files to the new rendering by
clicking, Settings > Rendering > Modernize after loading the old
session file. PyMOL will flip all the right settings to update
rendering. If the new code doesn't render properly, you can revert to
the old style rendering by typing:

 set use_shaders, 0

 set sphere_mode, 0

Please let us know how it goes.


-- Jason, Blaine & the PyMOL Team

Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120

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