Re: [PyMOL] Open Source PyMOL v1.5.0.1
Dear, I compiled PyMOL 1.5.0.1 from SVN revision 3979 on Centos 5 with python 2.7.1. and found "splash screen 1.3.x" too. Best, Zhijian Xu Troels Emtekær Linnet wrote: > Hi. > > I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with > python 2.6.6 from the RHEL repositories. > http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit > > Still splash screen 1.3.x ... Funny bug. > > Best > Troels > > > -- > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi all, I was wondering if the issue below on compiling molfile support has a fix? It looks like the include file was updated but not the C source. Thanks, Tim 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 > > > > -- > 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! > http://p.sf.net/sfu/learndevnow-dev2 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi, This also sounds like a graphics driver issue or issue with MESA (http://www.mesa3d.org/). Please ensure both are updated to their latest versions. Cheers, -- Jason On Wed, Feb 15, 2012 at 5:30 AM, Андрей Гончар wrote: > Hi all! > I've just installed a new version of PyMol, but when I select a > repersentation different to the default, it displays a blank screen > and returns > > unsupported IR in fragment shader 13 > unsupported IR in fragment shader 13 > unsupported IR in fragment shader 13 > unsupported IR in fragment shader 13 > unsupported IR in fragment shader 13 > > I run PyMol n Debian Squeeze x64, I have an integrated video > > Detected OpenGL version 2.0 or greater. Shaders available. > Detected GLSL version 1.20. > OpenGL graphics engine: > GL_VENDOR: Tungsten Graphics, Inc > GL_RENDERER: Mesa DRI Intel(R) G41 GEM 20091221 2009Q4 > GL_VERSION: 2.1 Mesa 7.7.1 > > -- > > Andrew Gonchar > > -- > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi. I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with python 2.6.6 from the RHEL repositories. http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit Still splash screen 1.3.x ... Funny bug. Best Troels -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi all! I've just installed a new version of PyMol, but when I select a repersentation different to the default, it displays a blank screen and returns unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 I run PyMol n Debian Squeeze x64, I have an integrated video Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: Tungsten Graphics, Inc GL_RENDERER: Mesa DRI Intel(R) G41 GEM 20091221 2009Q4 GL_VERSION: 2.1 Mesa 7.7.1 -- Andrew Gonchar -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
On Mon, Feb 13, 2012 at 2:27 PM, 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/). For those of you on openSUSE, I've updated the pymol packages in the openSUSE Build Service to this release. You can test this new version by visiting http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol and choosing the appropriate openSUSE release and architecture. -David -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
On Mon, Feb 13, 2012 at 02:27:54PM -0500, Jason Vertrees wrote: > Greetings, > ... I could make it build with python 2.6.6/2.7.2 but not with the default CentOS-5 python-2.4 version :( [tru@sillage pymol-1.5.0.1_3978]$ python setup.py install --prefix=/tmp/py24-pymol Traceback (most recent call last): File "setup.py", line 141, in ? import create_shadertext File "/home/tru/rpm/BUILD/pymol-1.5.0.1_3978/create_shadertext.py", line 8 with open(os.path.join(shaderdir, inputfile)) as f: ^ SyntaxError: invalid syntax ... > You should be able to pull and build just like normal. You will need Python > 2.7. argh :( Tru -- Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/ mailto:t...@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France -- Keep Your Developer Skills Current with LearnDevNow! 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! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
On 14/02/12 10:44, fukami...@chugai-pharm.co.jp wrote: > set cylinder_shader_ff_workaround thanks for that trick. It solved the problem. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Keep Your Developer Skills Current with LearnDevNow! 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! http://p.sf.net/sfu/learndevnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Dear Justin, It seems the problem I had. I've asked it to a Schrödinger expert and got an answer below. Try it. > You might be encountering a known problem with some Quadro cards. Can > you try the following command: > > set cylinder_shader_ff_workaround > > ... and to see if it fixes this problem? I'm using an alias below until the bug will be fixed. alias pymol="pymol -d 'set cylinder_shader_ff_workaround'" Hope this help. Takaaki Fukami -Original Message- From: Justin Lecher [mailto:j.lec...@fz-juelich.de] Sent: Tuesday, February 14, 2012 6:18 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1 On 14/02/12 09:29, Lecher, Justin wrote: > Hi Jason, > > I found a bug. If you set Display -> Quality -> Maximum Quality turns > the display around. That means the back is in the front and small, and > the front, larger parts are in the back. > > > justin To be more precise, it seems that this only occurs with sticks representation. All others are nice and super fast. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Keep Your Developer Skills Current with LearnDevNow! 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! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
On 14/02/12 09:29, Lecher, Justin wrote: > Hi Jason, > > I found a bug. If you set Display -> Quality -> Maximum Quality turns > the display around. That means the back is in the front and small, and > the front, larger parts are in the back. > > > justin To be more precise, it seems that this only occurs with sticks representation. All others are nice and super fast. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Keep Your Developer Skills Current with LearnDevNow! 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! http://p.sf.net/sfu/learndevnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi Jason, I found a bug. If you set Display -> Quality -> Maximum Quality turns the display around. That means the back is in the front and small, and the front, larger parts are in the back. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Keep Your Developer Skills Current with LearnDevNow! 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! http://p.sf.net/sfu/learndevnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Thanks! 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 > > (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 > > > > -- > Try before you buy = See our experts in action! > The most comprehensive online
Re: [PyMOL] Open Source PyMOL v1.5.0.1
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 smime.p7s Description: S/MIME Cryptographic Signature -- 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! http://p.sf.net/sfu/learndevnow-dev2
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi Jason, Thank you. Works well now. The speed improvements are very significant (Win64, GeForce GTX 560). Btw, the splash screens are still at version 1.3.x. Christoph On 2/13/2012 12:50 PM, Jason Vertrees wrote: > Hi Christoph, > > I just noticed that myself. I'll add the requisite files now. > > Cheers, > > -- Jason > > On Mon, Feb 13, 2012 at 3:47 PM, Christoph Gohlke wrote: >> >> >> On 2/13/2012 11:27 AM, 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 >>> >> >> That's good news! Thank you! >> >> It seems that several new files, which are included in the bz2 >> distribution, are missing in svn trunk. For example >> create_shadertext.py, modules\pymol\constants_palette.py and some files >> in data\shaders. >> >> http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/ >> >> Christoph >> >> -- >> 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! >> http://p.sf.net/sfu/learndevnow-dev2 >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- 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! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users A
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Christoph et. al, The changes have been pushed. Please let me know if you run into any other problems. Cheers, -- Jason On Mon, Feb 13, 2012 at 3:50 PM, Jason Vertrees wrote: > Hi Christoph, > > I just noticed that myself. I'll add the requisite files now. > > Cheers, > > -- Jason > > On Mon, Feb 13, 2012 at 3:47 PM, Christoph Gohlke wrote: >> >> >> On 2/13/2012 11:27 AM, 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 >>> >> >> That's good news! Thank you! >> >> It seems that several new files, which are included in the bz2 >> distribution, are missing in svn trunk. For example >> create_shadertext.py, modules\pymol\constants_palette.py and some files >> in data\shaders. >> >> http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/ >> >> Christoph >> >> -- >> 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! >> http://p.sf.net/sfu/learndevnow-dev2 >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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! http://p.sf.
Re: [PyMOL] Open Source PyMOL v1.5.0.1
Hi Christoph, I just noticed that myself. I'll add the requisite files now. Cheers, -- Jason On Mon, Feb 13, 2012 at 3:47 PM, Christoph Gohlke wrote: > > > On 2/13/2012 11:27 AM, 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 >> > > That's good news! Thank you! > > It seems that several new files, which are included in the bz2 > distribution, are missing in svn trunk. For example > create_shadertext.py, modules\pymol\constants_palette.py and some files > in data\shaders. > > http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/ > > Christoph > > -- > 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! > http://p.sf.net/sfu/learndevnow-dev2 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Open Source PyMOL v1.5.0.1
On 2/13/2012 11:27 AM, 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 > That's good news! Thank you! It seems that several new files, which are included in the bz2 distribution, are missing in svn trunk. For example create_shadertext.py, modules\pymol\constants_palette.py and some files in data\shaders. http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/ Christoph -- 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! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Open Source PyMOL v1.5.0.1
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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
