[PyMOL] Ray tracing with no GUI yields segmentation fault
Hello everyone, I wrote a python script where pymol performs some color changes, ray tracing and image export. The script works perfectly if I enable the GUI, however if I load pymol without the GUI (-c flag) I receive a segmentation fault error. I found out that this issue is resolved by commenting the line pymol.cmd.ray(640,640,300,-1). I'd like to solve this, so the script can run in a loop without opening the GUI every time. It may help to clarify that I'm running a LinuxMint14 machine (AMD64), with GCC compiler version 4.7.2. I appreciate any help. Ricardo. --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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] Pymol 1.3 and 1.6 compatability?
I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I have Pymol 1.3 opensource. I have a many session files (.pse) that I have made on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank you. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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] Ray tracing with no GUI yields segmentation fault
Hi Ricardo, you probably want to do this, without calling the ray command: cmd.png(image.png, 640, 640, dpi=300, ray=1) Also, your ray command sets antialias=300 and angle=-1, which I guess was not your intention. I'm not getting a segmentation fault with the latest SVN code using your command, though. Do you have any volume representation? Volume is not fully supported with ray tracing. Cheers, Thomas On 14 Jan 2014, at 13:36, Ricardo O. S. Soares rsoa...@fcfrp.usp.br wrote: Hello everyone, I wrote a python script where pymol performs some color changes, ray tracing and image export. The script works perfectly if I enable the GUI, however if I load pymol without the GUI (-c flag) I receive a segmentation fault error. I found out that this issue is resolved by commenting the line pymol.cmd.ray(640,640,300,-1). I'd like to solve this, so the script can run in a loop without opening the GUI every time. It may help to clarify that I'm running a LinuxMint14 machine (AMD64), with GCC compiler version 4.7.2. I appreciate any help. Ricardo. --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil -- Thomas Holder PyMOL Developer -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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] Pymol 1.3 and 1.6 compatability?
Hi Lapolla, Yes, you can keep your pymol v1.3 and v1.6. Just make sure that they have different names. You will also be able to open your old pse files. Cheers, Marcelo On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I have Pymol 1.3 opensource. I have a many session files (.pse) that I have made on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank you. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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] Pymol 1.3 and 1.6 compatability?
While you are updating, you might as well update to the very recently released version, 1.7. Engin On 1/14/14, 3:07 PM, Marcelo Marcet wrote: Hi Lapolla, Yes, you can keep your pymol v1.3 and v1.6. Just make sure that they have different names. You will also be able to open your old pse files. Cheers, Marcelo On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I have Pymol 1.3 opensource. I have a many session files (.pse) that I have made on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank you. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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] Pymol 1.3 and 1.6 compatability?
I thought that 1.7 was not free--that you had to pay for it. Not true? If 1.7 is free, could you give me a link? Thank you. From: Engin Özkan [eoz...@stanford.edu] Sent: Tuesday, January 14, 2014 3:10 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.3 and 1.6 compatability? While you are updating, you might as well update to the very recently released version, 1.7. Engin On 1/14/14, 3:07 PM, Marcelo Marcet wrote: Hi Lapolla, Yes, you can keep your pymol v1.3 and v1.6. Just make sure that they have different names. You will also be able to open your old pse files. Cheers, Marcelo On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I have Pymol 1.3 opensource. I have a many session files (.pse) that I have made on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank you. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrkk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=daca031becd601512885d60419da73dbf7ccbf20cb9f99487deb54f28f0af5db ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-usersk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=ce63051df7b3c767304cde0618ccee104099a2bb1aa512cf575a007d64d56644 Archives: https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.netk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=57c471dc756fc298f210fff0bafb2fd52b785d697c20ec2cce76d15f39f30859 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrkk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=daca031becd601512885d60419da73dbf7ccbf20cb9f99487deb54f28f0af5db ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-usersk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=ce63051df7b3c767304cde0618ccee104099a2bb1aa512cf575a007d64d56644 Archives: https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.netk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=57c471dc756fc298f210fff0bafb2fd52b785d697c20ec2cce76d15f39f30859 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. https://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrkk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=2SloLxdL42Y4DoIGAGdHX1Yw8Q1%2B2a8ypLfTV9Edqro%3D%0As=daca031becd601512885d60419da73dbf7ccbf20cb9f99487deb54f28f0af5db ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:
Re: [PyMOL] Pymol 1.3 and 1.6 compatability?
Hi Lapolla, The PyMOL source is available here: http://sourceforge.net/projects/pymol/ Hope this helps, Folmer 2014/1/14 Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu I thought that 1.7 was not free--that you had to pay for it. Not true? If 1.7 is free, could you give me a link? Thank you. From: Engin Özkan [eoz...@stanford.edu] Sent: Tuesday, January 14, 2014 3:10 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.3 and 1.6 compatability? While you are updating, you might as well update to the very recently released version, 1.7. Engin -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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] PyMOL v1.7 Released
Greetings, We are happy to announce the release of PyMOL v1.7.0.0! Official PyMOL sponsors can download ready-to-use installers from http://pymol.org/dsc/ip . The open-source code has been pushed to sourceforge svn (revision 4060) and a downloadable bz2 source file is also available from http://sf.net/p/pymol/. A few improvements include: Incentive PyMOL (for licensed users) * Improved labels, with connectors, backgrounds, outlines, and multiline text * Callouts for general labeling * 675 documented settings in the Settings Edit All GUI * New Find Wizard (CTRL-F) for locating objects in the object menu panel * ...and more Open Source and Incentive PyMOL * Added the focal_blur command * Added the get_renderer command to return information about the graphics renderer * Fetch command now takes SID and CID codes for PubChem * New selection keywords: metals, backbone, and sidechain * Access to settings and properties from the iterate/alter commands * Improved the PDB Loader GUI * Lots of Bugs Fixes AxPyMOL (for licensed users): * Built as a PowerPoint Add In * Option to embed data into the PowerPoint file * Supports PowerPoint PPTX files * Added support for presenting Maestro (.mae and .maegz) files * Added support for Windows 8, MS Office 2010 and 2013 (32- and 64-bit) * Support for shader-based rendering We encourage PyMOL sponsors to check out the internal documentation: * -- http://pymol.org/dsc/dokuwiki/doku.php?id=media:new17 We welcome any feedback and bug reports. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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] PyMOL, hydrogen bonds and PQR files with H-atoms
Dear PyMOL Users, I am writing a python script that utilizes the cmd.find_pairs and cmd.distance functions of the PyMOL API, in order to identify hydrogen bonds in a PQR file and calculate their properties. Since crystal structures rarely contain hydrogens, PyMOL guesses the position of hydrogen atoms for the identification of H-bonds (i.e. calculation of the D-H-A angle in find_pairs), with a process similar to the DSSP algorithm. However, my PQR files, generated by PDB2PQR, have their own hydrogen atoms. In cases such as this, does PyMOL use the H-atoms in the PQR file for the calculations, or does it sitll guess the position of H-atoms with its internal algorithm? Thank you in advance, Fotis Baltoumas -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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
