Hello all, Warren,

With the new PyMOL version, myself and others at the lab have found an issue with ray tracing of mesh representations causing memory utilization errors.

With parameters identical to those used in previous versions of PyMOL, 1.2r1 has crashed when ray tracing isomesh generated isosurface meshes. A memory allocation error is given, but a lack of memory does not appear to be the real issue, as PyMOL crashes long before all RAM is consumed, and the same error is given when we attempt to run this process on a machine with 12GB of RAM.

There have also been a few minor issues with the fetch command. Namely, we've seen intermitent inexplicable failure of the fetch command, while simultaneously using it in another version of PyMOL with no issue.

Also, some older scripts now need more specific import statements to utilize certain build-in PyMOL functionality. For example, I did not need to state "from pymol import selector" to use the selector.process() function in other versions of PyMOL, but this is not the case with the new version. Does this reflect changes in the cmd API setup?

Stuart Ballard


Message: 1
Date: Thu, 9 Jul 2009 13:34:53 -0700
From: "Warren DeLano" <warren@delsci.com>
Subject: [PyMOL] PyMOL 1.2r1 Released
To: <pymol-users@lists.sourceforge.net>
Content-Type: text/plain; charset="us-ascii"


Mac, Windows, and Linux builds for 1.2r1 were posted early this morning.
Current subscribers can download them via

Direct download: http://delsci.com/ip/12  or via online docs:

As usual, I recommend caution with upgrading.  Please don't upgrade
right before a major talk or presentation, unless you have time to test
everything thoroughly beforehand.  There were many last-minute changes
made after the last beta, so some glitches are to be expected.

Please try loading your important PyMOL session and show files into the
new version and report any serious problems.  At least one additional
revision of the 1.2 release is anticipated before the end of the summer.

Enabling information about the new capabilities of 1.2 will be
forthcoming over the next month, and will likely consist of a series of
screencast demonstrations and tutorials.  There is a lot of new stuff to