Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Hi Masataka, this is really a weird problem. I have none of CentOS, gcc45 or python2.4 so can't really simulate any of your setup. But from the message I would say it's related to the C preprocessor rather than the compiler or python itself. Also, a google search pointed me to this messages: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05501.html http://archives.neohapsis.com/archives/linux/immunix/2004-q1/0011.html The fact that it says macro fprintf suggests that fprintf has been replaced by a preprocessor macro, which may interfere with the macro that PyMOL defines in this case I guess. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? If it does not help, check if you have FormatGuard installed. Cheers, Thomas grantaka36 wrote, On 12/05/11 02:50: 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 2011/12/3 David Hall li...@cowsandmilk.net: the builds on https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or linux mint. -David On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com wrote: Could you please specified what exactly did the gcc 4.5 broke in Pymol? Maybe this is not the case for every linux distribution. Cheers, Marius 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com: Try Following this script. http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support Please report if you are successful. It would be interesting to see how it works on CentOS /T 2011/12/2 grantaka36 grantak...@gmail.com Referring the following, I'm trying to install PyMOL 1.4.1 with attached 'compile_pymol.sh', but no success. Would you please help to finish installation, or give me some advices? If information inadequate, please contact me. http://www.pymolwiki.org/index.php/Linux_Install - Requirements - Get latest Source from SVN - Compile and install - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44. Attached 'install_error.txt' gathers some information: - Original module files are in $HOME/install_module/pymol-archive - Intends to install in $HOME/pymol-svn - Original log has some Japanese messages so I added /* means ... */ Regards, Masataka -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] frames around code in PyMOLWiki
can we have frames around code blocks like before? Or am I the only one who misses them? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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)
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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] frames around code in PyMOLWiki
Thanks, Jason! Now it has borders, but no padding and background color and thus looks squeezed. I don't care how the exact look will be, but I'd like to see code containers more accentuated if possible. User css seems not to be enabled in the PyMOLWiki, right? http://www.mediawiki.org/wiki/Manual:$wgAllowUserCss Cheers, Thomas On 12/05/2011 03:08 PM, Jason Vertrees wrote: Hi Thomas, can we have frames around code blocks like before? Or am I the only one who misses them? This change was caused by the upgrade I made to the syntax highlighting plugin on the PyMOLWiki a few days ago. Check out the options here: http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi. I just modified the extension to allow this. If you want it then change: source lang=python to source lang=python enclose=div Cheers, -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] Select smart
Hi Troels, Jason - I've often wondered about these as well, so I've just updated the wiki page http://www.pymolwiki.org/index.php/Single-word_Selectors#More_selectors to reflect the single-word selectors from Selector.c. I think I got them all, but feel free to double check! Cheers, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329 New York, NY 10016 212-263-7898 On Dec 4, 2011, at 12:02 PM, Jason Vertrees wrote: HI Troels, pymol/layer3/Selector.c near line 355. Cheers, -- Jason 2011/12/4 Troels Emtekær Linnet tlin...@gmail.com: Hi. I sometimes see, that you can do select polymer select organic Is there a list somewhere with these keywords and what they select? Best Troels -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] Electron Density
Is there some way to show electron density at 6 sigma and above in pymol especially for metal ions like in Coot? Manas -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] Electron Density
I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] Electron Density
isomesh [mesh name], [map name], 6.0 Manas Sule wrote: Is there some way to show electron density at 6 sigma and above in pymol especially for metal ions like in Coot? Manas -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] Electron Density
Hi Manas, You have two options: use volumes (http://www.youtube.com/watch?v=tuAo_8-_HIc; http://pymol.org/volume) or isomesh myMesh, theMap, level=6 To change the isomesh level to 7.5 just do, isolevel myMesh, 7.5 Cheers, -- Jason On Mon, Dec 5, 2011 at 12:49 PM, Manas Sule sulema...@gmail.com wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] Electron Density
I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the selection about which you would like to see the electron density mesh. I haven't tested the contour limits, but it's larger than 10. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 12/5/2011 12:49 PM, Manas Sule wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] Select smart
Hi Jared. That is so cool! I missed that feature :-) Best T 2011/12/5 Sampson, Jared jared.samp...@nyumc.org Hi Troels, Jason - I've often wondered about these as well, so I've just updated the wiki page http://www.pymolwiki.org/index.php/Single-word_Selectors#More_selectorsto reflect the single-word selectors from Selector.c. I think I got them all, but feel free to double check! Cheers, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329 New York, NY 10016 212-263-7898 On Dec 4, 2011, at 12:02 PM, Jason Vertrees wrote: HI Troels, pymol/layer3/Selector.c near line 355. Cheers, -- Jason 2011/12/4 Troels Emtekær Linnet tlin...@gmail.com: Hi. I sometimes see, that you can do select polymer select organic Is there a list somewhere with these keywords and what they select? Best Troels -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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
