Thank you for the reports, and sorry to
hear you’re having trouble. Please allow me to draw your attention
to the Bug Reporter link on the PyMOL main page (www.pymol.org).
The direct link is:
One advantage of using the bug reporter
system is that you can submit accompanying script or data files which reproduce
With respect to meshes, rendering of
meshes is not generally broken in 1.2r1, so there must be something specific
about your input which is triggering the crash. We may need an example
file, or at least a PDB code with associated commands, to reproduce the
problem. Likewise, “fetch” is known not to be generally
broken, so we may need more information about reproducing the problem.
[For what it’s worth, I just
fetch 1fjf, async=0
runs fine with 1.2r1].
As for selector, it is not a supported
part of the supported Python “cmd” API, but rather, an internal
module. In other words, you should not ever need to be importing it.
Operationally speaking, the Python cmd. api is defined by the file “modules/pymol/api.py”,
and virtually all public symbols should be accessed as methods or submethods of
From: Stuart Ballard
Sent: Thursday, July 16, 2009 2:14
Subject: [PyMOL] PyMOL 1.2r1 error
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?
Date: Thu, 9 Jul 2009 13:34:53 -0700
From: "Warren DeLano" <firstname.lastname@example.org>
Subject: [PyMOL] PyMOL 1.2r1 Released
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