It worked. :-)

Troels Emtekær Linnet

2012/2/13 Justin Lecher <>
On 13.02.2012 20:27, Jason Vertrees wrote:
> Greetings,
> 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
> drivers.
> 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:
> Lines:
>    240% increase (81 FPS to 270 FPS)
> Spheres:
>    864% increase (28 FPS to 270 FPS)
> Sticks:
>    2100% increase (8 FPS to 180 FPS)
> Cartoon:
>    3757% increase (27 to 270 FPS)
> Surface:
>    2600% increase (10 to 270 FPS)
> Mesh:
>    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.
> Cheers,
> -- Jason, Blaine & the PyMOL Team

Hi Jason,

thanks for the work.

I cannot compile the molfile support:

x86_64-pc-linux-gnu-gcc -pthread -Ofast -pipe -ftracer -march=corei7-avx
-mtune=corei7-avx -mcx16 -msahf -mno-movbe -maes -mpclmul -mpopcnt
-mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mavx
-msse4.2 -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64
--param l2-cache-size=8192 -frecord-gcc-switches -g -funroll-loops
-Wimplicit-function-declaration -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
-Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2
-Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
-Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include
-Igenerated/src -I/usr/include/python2.7 -c
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_esp’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_npa’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_internals’
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1



Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
PyMOL-users mailing list (
Info Page: