Thanks!
It worked. :-)
Troels Emtekær Linnet
2012/2/13 Justin Lecher <j.lec...@fz-juelich.de>
> 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
> > (http://sourceforge.net/projects/pymol/).
> >
> > 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
> > (
> http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx
> ).
> > 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
> -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS
> -D_PYMOL_VMD_PLUGINS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS
> -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0
> -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
>
> build-2.7/temp.linux-x86_64-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
> ‘read_basis_metadata’:
> 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
>
>
> Thanks,
>
> justin
>
>
>
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