Re: [PyMOL] High Resolution Ray Tracing
Did you try using POV-Ray with PyMOL to do the ray tracing? renderer = 1 uses PovRay's renderer. This is Unix-only and you must have "povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and "tmp_pymol.png". Also works on Mac via Povray37UnofficialMacCmd but it needs to be in your path as "povray". Jim James Kress Ph.D., President The KressWorksR Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization "Engineering The Cure" C (248) 573-5499 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Stephen Kerry [mailto:stephen.kerr...@outlook.com] Sent: Monday, May 09, 2016 8:35 PM To: David Hall <li...@cowsandmilk.net> Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] High Resolution Ray Tracing Thank you for trying this out on a workstation with 128 GB and then 256 GB of RAM. It is much appreciated as I do not have easy access to that kind of computational power. The fact that you also get these segfaults with all of your RAM, suggests that this might be a PyMOL limitation, rather than a hardware issue. I have come to the conclusion that it is impossible to ray trace an image with an output resolution greater than 45 megapixels (7500 x 6000). Halving the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution. I was wondering if the developers have come across this upper limit too? I have a 2400 dpi printer, so I want to go with the highest dpi possible for the best quality. _ From: David Hall <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net> > Sent: 06 May 2016 19:17:38 To: Stephen Kerry Cc: pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] High Resolution Ray Tracing Feel free to send me the files off list. -David Hall On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com <mailto:stephen.kerr...@outlook.com> > wrote: Dear All, I have a protein complex scene that I need to create a large, high resolution (1200 dpi) ray traced image of, but am unable to do so as I always run out of memory at the end of the ray tracing process, with the following error: python2.7(972,0x7fff7397f300) malloc: *** mach_vm_map(size=18446744068907188224) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice this reserved for virtual memory, but no swap is actually used. Decreasing hash_max just increases the ray tracing time until the error at the end. Sometimes PyMOL will be terminated with this error, whilst at other times a transparent PNG is all that is produced. Is there a way to force PyMOL to use virtual memory to avoid these errors/crashes at the expense of processing time? If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB or more RAM, who would be able to render this ray traced image if I send the, the .pse file and .pml script off list? Takes about 10 mins to process. Cheers, Stephen -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! <https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ PyMOL-users mailing list ( <mailto:PyMOL-users@lists.sourceforge.net> PyMOL-users@lists.sourceforge.net) Info Page: <https://lists.sourceforge.net/lists/listinfo/pymol-users> https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Pl
Re: [PyMOL] Slow Pymol rendering
Glad I could help. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 573-5499 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Chen Zhao [mailto:chenzhaoh...@gmail.com] Sent: Saturday, May 07, 2016 12:51 AM To: jimkress...@kressworks.org Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Slow Pymol rendering Dear James, Thank you for your help! I tried versions 364.19, 352.79, 340.96, and none of them worked. Finally, I tried version 304.131 and it worked! (although my graphics card is listed as supported under all versions). Later I realized that command nvidia-detect could check which driver should be installed. And NVidia driver solved the slow pymol problem! Thanks for the help, Chen On Fri, May 6, 2016 at 1:23 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: The NVIDIA driver for x64 Linux is free and can be downloaded here: http://www.nvidia.com/download/driverResults.aspx/101818/en-us Or you can search here for something different: http://www.nvidia.com/Download/Find.aspx?lang=en-us Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 573-5499 <tel:%28248%29%20573-5499> Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Chen Zhao [mailto:chenzhaoh...@gmail.com <mailto:chenzhaoh...@gmail.com> ] Sent: Friday, May 06, 2016 10:50 AM To: pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net> Subject: [PyMOL] Slow Pymol rendering Dear all, I recently upgraded to Debian 8 and I compiled the source code for pymol 1.8.2.0. However, the graphics is really slow. The information that pymol prints out is as follows: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: nouveau GL_RENDERER: Gallium 0.4 on NVE7 GL_VERSION: 3.0 Mesa 10.3.2 Detected blacklisted graphics driver. Disabling shaders. Detected 8 CPU cores. Enabled multithreaded rendering. I am not sure whether it is related to the driver of my graphics card. I have a NVIDIA Corporation GK107GLM [Quadro K1000M] but I failed to install the non free Nvidia driver. I instead used the open source nouveau. I appreciate your inputs! Best, Chen -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ 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] Slow Pymol rendering
The NVIDIA driver for x64 Linux is free and can be downloaded here: http://www.nvidia.com/download/driverResults.aspx/101818/en-us Or you can search here for something different: http://www.nvidia.com/Download/Find.aspx?lang=en-us Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 573-5499 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Chen Zhao [mailto:chenzhaoh...@gmail.com] Sent: Friday, May 06, 2016 10:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Slow Pymol rendering Dear all, I recently upgraded to Debian 8 and I compiled the source code for pymol 1.8.2.0. However, the graphics is really slow. The information that pymol prints out is as follows: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: nouveau GL_RENDERER: Gallium 0.4 on NVE7 GL_VERSION: 3.0 Mesa 10.3.2 Detected blacklisted graphics driver. Disabling shaders. Detected 8 CPU cores. Enabled multithreaded rendering. I am not sure whether it is related to the driver of my graphics card. I have a NVIDIA Corporation GK107GLM [Quadro K1000M] but I failed to install the non free Nvidia driver. I instead used the open source nouveau. I appreciate your inputs! Best, Chen -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ 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] The Wiki appears outdated or in error
Bob, Thanks for the note. The pdf files you generated were quite nice. I just cannot get the quality of output you got using the PyMOL to dae to u3d to pdf path. All I get are washed out colors. No surface properties (shine, specular, etc.) at all. PDF3DReportGen is the only software I have found that can give me close to the representation I need. Even then, I have to use VMD, export to obj and then import to PDF3DReportGen to get good quality graphics. Very discouraging. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: Saturday, April 02, 2016 1:14 AM To: jimkress...@kressworks.org Cc: Thomas Holder <thomas.hol...@schrodinger.com>; pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error In case you are interested, Jim, Jmol will read (most/some) PyMOL session files, and Jmol can then create both an idtf for generating a u3d file, and a small sample TeX file also that can be used to create a PDF containing it. I had some interest in u3d back in 2009, when I wrote this exporter. You might be interested in my notes at the top of https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/export/_IdtfExporter.java Here are a few examples created using Jmol: http://chemapps.stolaf.edu/jmol/u3d/ As I recall, the TeX file is necessary in order to properly reproduce the viewport state. My conclusion was that u3d is an absolutely unmanageable file format. Its construction is totally obtuse, and the idtf->u3d converter has bugs that will probably never be fixed. I could be wrong, and in the intervening years it has improved, but my impression at the time was that it was an experimental format out of Adobe's research labs that never really made it and hasn't been developed much since then. Its inclusion in PDF file quite frankly takes the "P" out of "PDF." Bob Hanson -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ 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] The Wiki appears outdated or in error
Thanks. It works much better. I just wish I could find an alternative to MeshLab. The surfaces it generates in the u3d file are really poor. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization ENGINEERING THE CURE © (248) 605-8770 Learn More and Donate At: Website: http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, March 31, 2016 10:55 AM To: jimkress...@kressworks.org Cc: pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim, There is a beta version of Incentive PyMOL available for download from http://pymol.org/download/1811/ (version 1.8.1.1 BETA). Cheers, Thomas On 29 Mar 2016, at 23:30, James Kress <jimkress...@kressworks.org> wrote: > Does that mean it is in the pay version now? If yes, how do I get it, > through the normal download link? > > Jim > > James Kress Ph.D., President > The KressWorks® Foundation > An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization > ENGINEERING THE CURE © > (248) 605-8770 > > Learn More and Donate At: > Website: http://www.kressworks.org > Facebook: https://www.facebook.com/KressWorks.Foundation/ > Twitter: @KressWorksFnd > > Confidentiality Notice | This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential or proprietary information. Any unauthorized > review, use, disclosure or distribution is prohibited. If you are not > the intended recipient, immediately contact the sender by reply e-mail > and destroy all copies of the original message. > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Sunday, March 27, 2016 4:10 PM > To: pymol-users <pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] The Wiki appears outdated or in error > > Hi Jared, > > Thanks a lot for the patch. Applied to SVN rev 4154. > > Cheers, > Thomas > > On 25 Mar 2016, at 20:03, Sampson, Jared M. > <jms2...@cumc.columbia.edu> > wrote: > >> Hi Jim - >> >> Here's a patch for Open Source PyMOL (rev4153) that adds the > "collada_background_box" setting (default=0). If you're using Open > Source PyMOL and are up to applying it and rebuilding, feel free to use it. > Otherwise, I already sent it to Thomas, so hopefully it will be > incorporated into SVN and Incentive PyMOL soon. >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Columbia University >> >>> On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. > <jms2...@cumc.columbia.edu> wrote: >>> >>> Hi Jim - >>> >>>> When I >>>> >>>> set geometry_export_mode, 1 >>>> >>>> in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. >>> >>> I can confirm that this happens for me, too. I guess maybe Meshlab > requires the camera? >>> >>> As a workaround, you can go back to the previous version with > collada_geometry_mode=1 and simply delete the box. You can do this > within Meshlab by using the "Select Connected Components in a region" > tool to select a corner the box, then clicking the "Delete the current > set of selected faces and all the vertices surrounded by that faces" > button (see attached screenshot). Then, if you zoom in (the box is > 100x larger than the largest dimension of the scene), your scene will be there. >>> >>> I'm working on a patch right now to exclude the bounding background >>> box > from default COLLADA output and make it optional via a new > `collada_background_box` setting. >>> >>> Sorry for the confusion, hope this clears it up. >>> >>> Cheers, >>> Jared >>> >>> -- >>> Jared Sampson >>> Columbia University >>> >> >> > - -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ 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] The Wiki appears outdated or in error
Does that mean it is in the pay version now? If yes, how do I get it, through the normal download link? Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization ENGINEERING THE CURE © (248) 605-8770 Learn More and Donate At: Website: http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Sunday, March 27, 2016 4:10 PM To: pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jared, Thanks a lot for the patch. Applied to SVN rev 4154. Cheers, Thomas On 25 Mar 2016, at 20:03, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote: > Hi Jim - > > Here's a patch for Open Source PyMOL (rev4153) that adds the "collada_background_box" setting (default=0). If you're using Open Source PyMOL and are up to applying it and rebuilding, feel free to use it. Otherwise, I already sent it to Thomas, so hopefully it will be incorporated into SVN and Incentive PyMOL soon. > > Cheers, > Jared > > -- > Jared Sampson > Columbia University > >> On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote: >> >> Hi Jim - >> >>> When I >>> >>> set geometry_export_mode, 1 >>> >>> in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. >> >> I can confirm that this happens for me, too. I guess maybe Meshlab requires the camera? >> >> As a workaround, you can go back to the previous version with collada_geometry_mode=1 and simply delete the box. You can do this within Meshlab by using the "Select Connected Components in a region" tool to select a corner the box, then clicking the "Delete the current set of selected faces and all the vertices surrounded by that faces" button (see attached screenshot). Then, if you zoom in (the box is 100x larger than the largest dimension of the scene), your scene will be there. >> >> I'm working on a patch right now to exclude the bounding background box from default COLLADA output and make it optional via a new `collada_background_box` setting. >> >> Sorry for the confusion, hope this clears it up. >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Columbia University >> > > -- --- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140 ___ 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ 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] The Wiki appears outdated or in error
Thanks! Jim James Kress Ph.D., President The KressWorksR Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization "Engineering The Cure" C (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Friday, March 25, 2016 3:03 PM To: jimkress...@kressworks.org Cc: pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - Here's a patch for Open Source PyMOL (rev4153) that adds the "collada_background_box" setting (default=0). If you're using Open Source PyMOL and are up to applying it and rebuilding, feel free to use it. Otherwise, I already sent it to Thomas, so hopefully it will be incorporated into SVN and Incentive PyMOL soon. Cheers, Jared -- Jared Sampson Columbia University On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu <mailto:jms2...@cumc.columbia.edu> > wrote: Hi Jim - When I set geometry_export_mode, 1 in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. I can confirm that this happens for me, too. I guess maybe Meshlab requires the camera? As a workaround, you can go back to the previous version with collada_geometry_mode=1 and simply delete the box. You can do this within Meshlab by using the "Select Connected Components in a region" tool to select a corner the box, then clicking the "Delete the current set of selected faces and all the vertices surrounded by that faces" button (see attached screenshot). Then, if you zoom in (the box is 100x larger than the largest dimension of the scene), your scene will be there. I'm working on a patch right now to exclude the bounding background box from default COLLADA output and make it optional via a new `collada_background_box` setting. Sorry for the confusion, hope this clears it up. Cheers, Jared -- Jared Sampson Columbia University -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___ 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] The Wiki appears outdated or in error
Hi Jared, Thanks for the information. There was no screen shot attached, however. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Thursday, March 24, 2016 2:26 PM To: jimkress...@kressworks.org Cc: Sampson, Jared M. <jms2...@cumc.columbia.edu>; pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - When I set geometry_export_mode, 1 in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. I can confirm that this happens for me, too. I guess maybe Meshlab requires the camera? As a workaround, you can go back to the previous version with collada_geometry_mode=1 and simply delete the box. You can do this within Meshlab by using the "Select Connected Components in a region" tool to select a corner the box, then clicking the "Delete the current set of selected faces and all the vertices surrounded by that faces" button (see attached screenshot). Then, if you zoom in (the box is 100x larger than the largest dimension of the scene), your scene will be there. I'm working on a patch right now to exclude the bounding background box from default COLLADA output and make it optional via a new `collada_background_box` setting. Sorry for the confusion, hope this clears it up. Cheers, Jared -- Jared Sampson Columbia University On Mar 24, 2016, at 1:05 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: Hi Jared, When I set geometry_export_mode, 1 in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. Is there an alternative to MeshLab I can use to generate the u3d file? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 23, 2016 10:53 PM To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> Cc: pymol-users <pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - This is something we've been talking about changing. The entire scene as viewed within PyMOL is inside that block, including the camera position. (The interior surface of the block itself provides the background color of the scene.) Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing. To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae. Hope that helps! Cheers, Jared P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future. Jared Sampson Columbia University On Mar 23, 2016, at 8:26 PM, James Kress < <mailto:jimkress...@kressworks.org> jimkress...@kressworks.org> wrote: I installed v 1.8.0.6 When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block. What do I need to do in PyMOL to export my DNA structure? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit O
Re: [PyMOL] The Wiki appears outdated or in error
Hi Jared, When I set geometry_export_mode, 1 in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. Is there an alternative to MeshLab I can use to generate the u3d file? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 23, 2016 10:53 PM To: jimkress...@kressworks.org Cc: pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - This is something we've been talking about changing. The entire scene as viewed within PyMOL is inside that block, including the camera position. (The interior surface of the block itself provides the background color of the scene.) Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing. To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae. Hope that helps! Cheers, Jared P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future. Jared Sampson Columbia University On Mar 23, 2016, at 8:26 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: I installed v 1.8.0.6 When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block. What do I need to do in PyMOL to export my DNA structure? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Tuesday, March 22, 2016 1:40 PM To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> Cc: pymol-users <pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability. You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF. Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: <http://www.pymolwiki.org/index.php/Category:Installation> http://www.pymolwiki.org/index.php/Category:Installation. Cheers, Jared -- Jared Sampson Columbia University On Mar 21, 2016, at 5:46 PM, James Kress < <mailto:jimkress...@kressworks.org> jimkress...@kressworks.org> wrote: Hi Jared, The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type. Here is the message PyMOL generates: PyMOL>save output_no_H2O.dae Save-Warning: Unrecognized file type -- defaulting to PDB format. Save: wrote "output_no_H2O.dae". I get the same error message if I use the command ‘save output_no_H2O.dae’ Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and D
Re: [PyMOL] The Wiki appears outdated or in error
I installed v 1.8.0.6 When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block. What do I need to do in PyMOL to export my DNA structure? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Tuesday, March 22, 2016 1:40 PM To: jimkress...@kressworks.org Cc: pymol-users <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability. You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF. Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: http://www.pymolwiki.org/index.php/Category:Installation. Cheers, Jared -- Jared Sampson Columbia University On Mar 21, 2016, at 5:46 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: Hi Jared, The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type. Here is the message PyMOL generates: PyMOL>save output_no_H2O.dae Save-Warning: Unrecognized file type -- defaulting to PDB format. Save: wrote "output_no_H2O.dae". I get the same error message if I use the command ‘save output_no_H2O.dae’ Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 16, 2016 2:28 PM To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> Cc: pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi James - If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format. As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D. When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow elements to describe the triangles, which are a more general, verbose description than the more concise and output generated with the default setting). Hope that helps. Cheers, Jared -- Jared Sampson Columbia University On Mar 12, 2016, at 11:24 PM, James Kress < <mailto:jimkress...@kressworks.org> jimkress...@kressworks.org> wrote: Among the export functions, a particular interest of mine is the as a idtf file as "precursor" for a 3d pdf mentioned at <http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf where I experience difficulties I want to address here. While the export via the CLI works fine for creating a *.png picture or a VRML *.wrl-geometry, the similar export as *.idtf creates only a header to describe the scenery, but not the (expected) s
Re: [PyMOL] The Wiki appears outdated or in error
Hi Jared, The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type. Here is the message PyMOL generates: PyMOL>save output_no_H2O.dae Save-Warning: Unrecognized file type -- defaulting to PDB format. Save: wrote "output_no_H2O.dae". I get the same error message if I use the command ‘save output_no_H2O.dae’ Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 16, 2016 2:28 PM To: jimkress...@kressworks.org Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi James - If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format. As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D. When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow elements to describe the triangles, which are a more general, verbose description than the more concise and output generated with the default setting). Hope that helps. Cheers, Jared -- Jared Sampson Columbia University On Mar 12, 2016, at 11:24 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: Among the export functions, a particular interest of mine is the as a idtf file as "precursor" for a 3d pdf mentioned at <http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf where I experience difficulties I want to address here. While the export via the CLI works fine for creating a *.png picture or a VRML *.wrl-geometry, the similar export as *.idtf creates only a header to describe the scenery, but not the (expected) spheres and tubes to represent atoms and molecular bonds. The file generated is the same, regardless if I request the data export via save /home/user directory/target directory/test.idtf or the recommended save /home/user directory/target directory/test.idtf,* Marking/highlighting the molecule in question does not alter the situation. The relative orientation of the model in regard to the observer is provided, however, in the programs command line, like 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00 In addition, there is no *.tex file written -- well in contrast to the pymol-wiki page -- that I would expect to be created in the very same directory, too. (This is contrast to jmol offering export as *.idtf while simultaneously writing a *.tex file, too.) Should I look up in a different directory instead? May be a mistake during the installation be a reason why I do not obtain (yet) a functional *.idtf? Do I need to load another / an additional plugin to enlarge the export functions? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. <http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140__
Re: [PyMOL] The Wiki appears outdated or in error
HI Jared, Thank you for your response. I will give it a try! Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 16, 2016 2:28 PM To: jimkress...@kressworks.org Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi James - If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format. As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D. When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow elements to describe the triangles, which are a more general, verbose description than the more concise and output generated with the default setting). Hope that helps. Cheers, Jared -- Jared Sampson Columbia University On Mar 12, 2016, at 11:24 PM, James Kress <jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> > wrote: Among the export functions, a particular interest of mine is the as a idtf file as "precursor" for a 3d pdf mentioned at <http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf where I experience difficulties I want to address here. While the export via the CLI works fine for creating a *.png picture or a VRML *.wrl-geometry, the similar export as *.idtf creates only a header to describe the scenery, but not the (expected) spheres and tubes to represent atoms and molecular bonds. The file generated is the same, regardless if I request the data export via save /home/user directory/target directory/test.idtf or the recommended save /home/user directory/target directory/test.idtf,* Marking/highlighting the molecule in question does not alter the situation. The relative orientation of the model in regard to the observer is provided, however, in the programs command line, like 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00 In addition, there is no *.tex file written -- well in contrast to the pymol-wiki page -- that I would expect to be created in the very same directory, too. (This is contrast to jmol offering export as *.idtf while simultaneously writing a *.tex file, too.) Should I look up in a different directory instead? May be a mistake during the installation be a reason why I do not obtain (yet) a functional *.idtf? Do I need to load another / an additional plugin to enlarge the export functions? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. <http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___> http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___ PyMOL-users mailing list ( <mailto:PyMOL-users@lists.sourceforge.net> PyMOL-users@lists.sourceforge.net) Info Page: <https://lists.sourceforge.net/lists/lis
[PyMOL] IDTF and tex files
I finally got an IDTF file but no pymol.tex file. Why no tex file, is PYMOL IDTF still limited to cartoons only and if so, are there any plans to go beyond that? Thanks. Jim James Kress Ph.D., President The KressWorksR Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization "Engineering The Cure" C (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___ 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] The Wiki appears outdated or in error
Among the export functions, a particular interest of mine is the as a idtf file as "precursor" for a 3d pdf mentioned at http://www.pymolwiki.org/index.php/3d_pdf where I experience difficulties I want to address here. While the export via the CLI works fine for creating a *.png picture or a VRML *.wrl-geometry, the similar export as *.idtf creates only a header to describe the scenery, but not the (expected) spheres and tubes to represent atoms and molecular bonds. The file generated is the same, regardless if I request the data export via save /home/user directory/target directory/test.idtf or the recommended save /home/user directory/target directory/test.idtf,* Marking/highlighting the molecule in question does not alter the situation. The relative orientation of the model in regard to the observer is provided, however, in the programs command line, like 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00 In addition, there is no *.tex file written -- well in contrast to the pymol-wiki page -- that I would expect to be created in the very same directory, too. (This is contrast to jmol offering export as *.idtf while simultaneously writing a *.tex file, too.) Should I look up in a different directory instead? May be a mistake during the installation be a reason why I do not obtain (yet) a functional *.idtf? Do I need to load another / an additional plugin to enlarge the export functions? Thanks. Jim James Kress Ph.D., President The KressWorksR Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization "Engineering The Cure" C (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: <https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___ 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
