Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Dear Thomas and all advisers, Thanks for all, I've got installed pymol in CentOS5 from EPEL repository. Turning back to the package list by Yum Extender (yumex), I found 'pymol' appeared as http://lockerz.com/s/162790999 after http://lockerz.com/s/162790733 cf.) - Might need installed 'epel*' # rpm -i http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm - 'yumex' can be installed: # yum install yumex Can I add this information to pymolwiki (Need an account) ? http://www.pymolwiki.org/index.php/Linux_Install After PyMOL running, console says: freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' but I will try to check and contact here as another issue if not succeeded. Regards, Masataka 2011/12/6 grantaka36 grantak...@gmail.com: Dear Thomas, Thanks for good pointing for the weird problem, which I couldn't notice at all. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? I'm afraid, I know not related PyMOL itself, but I wish to know how to do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches. And Zhijian and Andreas, Thank you for advices through your experiences, I will pursue at first as Thomas advised. Regards, Masataka 2011/12/5 Andreas Förster docandr...@gmail.com: Dear Masataka, a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1. If version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I would urge you, to upgrade as well. RHEL and CentOS are rock-solid operating systems, but their libraries and dependencies show their age. Andreas On 05/12/2011 1:50, grantaka36 wrote: Hi, Marius, Troels and David, I appreciate very much for guiding, tried in three ways but no success currently. - I also think some difference on distributions (CentOS 5 here,) trapped at function 'IsosurfGetRange' Does anyone have information to workaround? - Do you think if any dependency on Python version (2.4.3 here)? Attached '20111205_script_and_error.zip' is for information sharing: - 'install_pymol.sh' : followed by below, some package name modified for CentOS http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support - 'install_pymol_sh_error.txt' layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro fprintf layer0/Isosurf.c: In function 'IsosurfGetRange': - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5 instead of 4.4 - 'install_pymol_gcc45_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf - 'compile_pymol.sh' : again by initial trying http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source - 'compile_pymol_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf Regards, Masataka -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] Installation PyMOL failure in Linux (CentOS)
Hi Masataka, Thanks for all, I've got installed pymol in CentOS5 from EPEL repository. Turning back to the package list by Yum Extender (yumex), I found 'pymol' appeared as http://lockerz.com/s/162790999 after http://lockerz.com/s/162790733 cf.) - Might need installed 'epel*' # rpm -i http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm - 'yumex' can be installed: # yum install yumex Can I add this information to pymolwiki (Need an account) ? http://www.pymolwiki.org/index.php/Linux_Install sure, that would be great. But first try to solve the freeglut issue. Jason can give you an account for the PyMOLWiki. Or I can update the Linux_Install page. After PyMOL running, console says: freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' but I will try to check and contact here as another issue if not succeeded. do you have a graphics driver with direct rendering support installed? glxinfo | grep direct Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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] Reading Protein Structure File (PSF)
Hi PyMOLers, Can anybody tell me if there's a way to read in a protein structure file (PSF). This is a common file format in simulation programs such as CHARMM and NAMD and basically gives similar information to the PDB file. Any suggestions would be greatly appreciated. Thank you for your time. Sean -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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] Reading Protein Structure File (PSF)
Hi Sean, The .psf file format is for a topological desription (bonds, angles, etc), not for coordinates afaik. Cheers, Tsjerk On Dec 7, 2011 6:25 PM, Sean Law magic...@hotmail.com wrote: Hi PyMOLers, Can anybody tell me if there's a way to read in a protein structure file (PSF). This is a common file format in simulation programs such as CHARMM and NAMD and basically gives similar information to the PDB file. Any suggestions would be greatly appreciated. Thank you for your time. Sean -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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] Reading Protein Structure File (PSF)
Tsjerk, You are correct that the PSF file only has that information. I should have mentioned that I plan to load a simulation trajectory file (DCD) into this PSF/PyMOL object. Thanks Sean Date: Wed, 7 Dec 2011 18:28:28 +0100 Subject: Re: [PyMOL] Reading Protein Structure File (PSF) From: tsje...@gmail.com To: magic...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Sean, The .psf file format is for a topological desription (bonds, angles, etc), not for coordinates afaik. Cheers, Tsjerk On Dec 7, 2011 6:25 PM, Sean Law magic...@hotmail.com wrote: Hi PyMOLers, Can anybody tell me if there's a way to read in a protein structure file (PSF). This is a common file format in simulation programs such as CHARMM and NAMD and basically gives similar information to the PDB file. Any suggestions would be greatly appreciated. Thank you for your time. Sean -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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] Installation PyMOL failure in Linux (CentOS)
Hi Masataka, Thanks for all, I've got installed pymol in CentOS5 from EPEL repository. Turning back to the package list by Yum Extender (yumex), I found 'pymol' appeared as http://lockerz.com/s/162790999 after http://lockerz.com/s/162790733 cf.) - Might need installed 'epel*' # rpm -i http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm - 'yumex' can be installed: # yum install yumex Can I add this information to pymolwiki (Need an account) ? http://www.pymolwiki.org/index.php/Linux_Install I'd like to figure out the minimal efford to get PyMOL installed this way before adding it to the wiki. I guess yumex is not necessary, does this command work as well? yum --enablerepo=epel install pymol Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ 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
