From: grantaka36 <gra...@gm...> - 2011-12-02 07:19:24
Attachments:
install_error.txt
compile_pymol.sh
|
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 |
From: Marius R. <mar...@gm...> - 2011-12-02 08:59:43
|
Hello, The latest revision 3971 compiles without problems with gcc 4.5.1 on Fedora 14. I usually install all the dependencies with yum. My suggestion would be to try compiling with gcc4.5. Marius On Fri, Dec 2, 2011 at 8:19 AM, grantaka36 <gra...@gm...> wrote: > 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 > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Troels E. L. <tl...@gm...> - 2011-12-02 15:10:00
|
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 <gra...@gm...> > 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 > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Marius R. <mar...@gm...> - 2011-12-02 15:21:58
|
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 <tl...@gm...>: > 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 <gra...@gm...> >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Troels E. L. <tl...@gm...> - 2011-12-02 15:30:02
|
Hi Marius. The last test I had on a Ubuntu/Mint box (1 month ago), it would not compile with gcc 4.5. So, it is necessary to change to gcc 4.4 I have made a script that auto compile on Ubuntu/Mint. I have not checked the last release with hcc 4.5 I have not tried CentOS. It would be interesting to have a compile script, for RPM package system. I do not know if gcc 4.5 works on CentOS. Best Troels 2011/12/2 Marius Retegan <mar...@gm...> > 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 <tl...@gm...>: > > 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 <gra...@gm...> > >> > >> 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 > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > > > > > > > > > ------------------------------------------------------------------------------ > > 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 (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > |
From: David H. <li...@co...> - 2011-12-02 16:14:19
|
the builds on https://build.opensuse.org/package/show?package=pymol&project=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 <mar...@gm...> 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 <tl...@gm...>: >> 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 <gra...@gm...> >>> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: grantaka36 <gra...@gm...> - 2011-12-05 01:50:24
Attachments:
20111205_script_and_error.zip
|
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...@co...>: > the builds on https://build.opensuse.org/package/show?package=pymol&project=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 <mar...@gm...> 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 <tl...@gm...>: >>> 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 <gra...@gm...> >>>> >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> ------------------------------------------------------------------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... |
From: zjxu <zj...@ma...> - 2011-12-05 06:26:54
|
Dear Masataka, Will you try update python 2.4.3 to python 2.6 or later? Pymol 1.4.1 works well on my centos5.4. In my case, I both have python 2.7.1 and pytnon 2.4 in the system, and use python 2.7.1 to compile pymol. In addition, the gcc version is 4.1.2. Hope it helps, Zhijian Xu 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 > > > 2011/12/3 David Hall <li...@co...>: > >> the builds on https://build.opensuse.org/package/show?package=pymol&project=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 <mar...@gm...> 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 <tl...@gm...>: >>> >>>> 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 <gra...@gm...> >>>> >>>>> 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 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------------ >>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <sp...@us...> - 2011-12-05 09:03:48
|
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/pym...@li.../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...@co...>: >> the builds on https://build.opensuse.org/package/show?package=pymol&project=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 <mar...@gm...> 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 <tl...@gm...>: >>>> 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 <gra...@gm...> >>>>> 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 |
From: Andreas F. <doc...@gm...> - 2011-12-05 11:35:59
|
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 |
From: grantaka36 <gra...@gm...> - 2011-12-06 10:39:56
|
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 <doc...@gm...>: > 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 |
From: grantaka36 <gra...@gm...> - 2011-12-07 13:09:41
|
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 <gra...@gm...>: > 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 <doc...@gm...>: >> 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 |
From: Thomas H. <sp...@us...> - 2011-12-07 13:19:36
|
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 |
From: Thomas H. <sp...@us...> - 2011-12-07 23:08:55
|
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 |
From: grantaka36 <gra...@gm...> - 2011-12-08 05:40:14
|
Dear Thomas, > yum --enablerepo=epel install pymol Yes, above also worked fine, so 'yumex' is not always needed. Thanks. I've got received a pymolwiki account by Jason, and will add minimal and sufficient information, after if cleared graphic driver problem. Regards, Masataka 2011/12/8 Thomas Holder <sp...@us...>: > 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 |
From: Martin H. <ma...@bl...> - 2011-12-08 14:49:41
|
Dear PyMOL List I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation of tryptophan to phenylalanin. If the sidechain is mutated from W to F, its reasonable to assume that the plane of the phenyl moiety of F would/should/could/might lie in the same plane as the indol part of the W if there was such a protein. Would it be possible to scriptically adjust the F side chain, after mutation, such that it lies in the W plane? Of course, this becomes ambiguous when, say, a A is mutated to a D, because what would then be the reference for the D side chain? However, N to D would be another case, where it would be desired to have the D end group be in as much overlay with the former N end group as possible. Any ideas on how this might be afforded? Probably not a one-liner though. Kind regards Martin |
From: Troels E. L. <tl...@gm...> - 2011-12-08 15:12:10
|
Can this plugin solve it: http://www.pymolwiki.org/index.php/Rotamer_Toggle Note, that you have to collect the script yourself, and replace the original pymol menu.py file. Not a easy solution to problem. Note, it the script: http://www.pymolwiki.org/index.php/Rotkit You can mutate through a command line, and selecting which rotamer to use. But that would not solve your problem of specifying which plane to select. In http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis are some more examples of mutating in PyMOL and get the pKa for the mutations. Best Troels 2011/12/8 Martin Hediger <ma...@bl...> > Dear PyMOL List > I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation > of tryptophan to phenylalanin. If the sidechain is mutated from W to F, > its reasonable to assume that the plane of the phenyl moiety of F > would/should/could/might lie in the same plane as the indol part of the > W if there was such a protein. > Would it be possible to scriptically adjust the F side chain, after > mutation, such that it lies in the W plane? > Of course, this becomes ambiguous when, say, a A is mutated to a D, > because what would then be the reference for the D side chain? However, > N to D would be another case, where it would be desired to have the D > end group be in as much overlay with the former N end group as possible. > > Any ideas on how this might be afforded? Probably not a one-liner though. > > Kind regards > Martin > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |