Re: [COOT] problem with install on new Macbook Pro (OS X 10.5) **SOLVED**
On Jun 5, 2009, at 9:53 PM, William Scott wrote: Two more thoughts: 1. What shell are you using? if it is tcsh, then you need to source a different file, i.e., source /usr/local/xtal/coot/bin/init.csh This solved it. However I am in fact using tcsh, just as I was on my previous Mac. On the previous Mac the standard sourcing of the init.sh file did not raise any issues though so tcsh is not the only culprit. Being a lazy person, I wanted to then correct the coot wrapper script to reflect my shell requirements so that I can invoke coot with only one command. In the end this worked: (the script has only 6 lines, so be careful if you copy and paste it as the wrapped lines may have copied as new lines.) #!/bin/csh -f source /usr/local/xtal/coot/bin/init.csh setenv COOT_REFMAC_LIB_DIR /usr/local/xtal/coot/share/coot/lib setenv COOT_PYTHON_DIR /usr/local/xtal/coot/share/coot/python setenv PYTHONPATH /usr/local/xtal/coot/lib/python25.zip:/usr/local/ xtal/coot/lib/python2.5:/usr/local/xtal/coot/lib/python2.5/plat- darwin:/usr/local/xtal/coot/lib/python2.5/plat-mac:/usr/local/xtal/ coot/lib/python2.5/plat-mac/lib-scriptpackages:/usr/local/xtal/coot/ lib/python2.5/lib-tk:/usr/local/xtal/coot/lib/python2.5/lib-dynload:/ usr/local/xtal/coot/lib/python2.5/site-packages:/usr/local/xtal/coot/ lib/python2.5/site-packages/Numeric:/usr/local/xtal/coot/lib/python2.5/ site-packages/gtk-2.0:/usr/local/xtal/coot/share/coot/python /usr/local/xtal/coot/bin/coot-real Bill, perhaps you can tell me if my having removed the $@ and $PYTHONPATH in the original wrapper will be a problem down the line. Since my environment does not have a pre-existing $PYTHONPATH, the script would abort at this line when it was included. I suppose there is a better syntax for the script that would allow for the possibility of a $PYTHONPATH... but it is beyond me. Thanks to all who responded with their input. -Jason because the syntax is not compatible with the other shells. 2. Maybe updating to the most recent X11 will help: http://xquartz.macosforge.org/trac/ Sometimes Apple's updates will clobber parts of this, and regress it to older versions of some files, which makes a mess, so if in doubt, it is always a good idea to reinstall X11. I try to compile these things with the most current X11, which might lead to incompatibilities. HTH, Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jun 5, 2009, at 9:54 AM, Jason Greenwald wrote: Thank you Bill and also other helpful folks. I should have mentioned this my original post, but when I issue the source command (which of course is also done by the coot wrapper shell script) I get the result: Illegal variable name. And coot still does not work. Perhaps something that is also of interest is that a handful of the icons are visible in the graphics window: Clear pending picks Delete item Recover session Map color Bond color Background color Preferences About and a few others. However, some others have an x icon (like for a missing image while many (the majority?) others simply have nothing to replace the missing icon. In the meantime I am using the COOT.app package from the CCP4 download site, so if anyone knows how to save more than one session using this installation, I would be happy to hear it. Cheers. Jason On Jun 5, 2009, at 6:35 PM, William G. Scott wrote: Hi Jason: For some reason that I don't understand, some users find they need to issue the command source /usr/local/xtal/coot/bin/init.sh prior to issuing the command coot (coot in this context actually invokes a wrapper shell script that has that first source command in it, so that is why I don't understand why it isn't working. If someone who is experiencing this problem feels like trying an experiment, just edit that shell script file /usr/local/xtal/coot/bin/coot and after the source line, add a line like sleep 5 before the line that invokes coot-real. I can't reproduce the problem, so I can't test this.) Sorry for the inconvenience. Bill On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg'
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Hi, The CCP4 download page has a proper package, which works, despite being an older version. I had problems with his binaries too, (from this web page: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X ) ...but the best way for me was to use his fink installation method (fink seems to be a wrapper for apt-get, as far as I can tell): http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled Synopsis: 1) Install fink 2) Edit /sw/etc/fink.conf 3) Update fink 4) Install Coot fink -b install coot ...which should give you a new binary: /sw/bin/coot This is a synopsis, but there are full instructions on the web page, starting here: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled#Before_you_begin I hope this helps Mark P.S. Thanks for the binaries Bill! 2009/6/5 Jason Greenwald jason.greenw...@phys.chem.ethz.ch: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg' Any ideas? Thanks in advance, Jason -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Hi Jason: For some reason that I don't understand, some users find they need to issue the command source /usr/local/xtal/coot/bin/init.sh prior to issuing the command coot (coot in this context actually invokes a wrapper shell script that has that first source command in it, so that is why I don't understand why it isn't working. If someone who is experiencing this problem feels like trying an experiment, just edit that shell script file /usr/ local/xtal/coot/bin/coot and after the source line, add a line like sleep 5 before the line that invokes coot-real. I can't reproduce the problem, so I can't test this.) Sorry for the inconvenience. Bill On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg' Any ideas? Thanks in advance, Jason
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Thank you Bill and also other helpful folks. I should have mentioned this my original post, but when I issue the source command (which of course is also done by the coot wrapper shell script) I get the result: Illegal variable name. And coot still does not work. Perhaps something that is also of interest is that a handful of the icons are visible in the graphics window: Clear pending picks Delete item Recover session Map color Bond color Background color Preferences About and a few others. However, some others have an x icon (like for a missing image while many (the majority?) others simply have nothing to replace the missing icon. In the meantime I am using the COOT.app package from the CCP4 download site, so if anyone knows how to save more than one session using this installation, I would be happy to hear it. Cheers. Jason On Jun 5, 2009, at 6:35 PM, William G. Scott wrote: Hi Jason: For some reason that I don't understand, some users find they need to issue the command source /usr/local/xtal/coot/bin/init.sh prior to issuing the command coot (coot in this context actually invokes a wrapper shell script that has that first source command in it, so that is why I don't understand why it isn't working. If someone who is experiencing this problem feels like trying an experiment, just edit that shell script file /usr/local/xtal/coot/bin/coot and after the source line, add a line like sleep 5 before the line that invokes coot-real. I can't reproduce the problem, so I can't test this.) Sorry for the inconvenience. Bill On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg' Any ideas? Thanks in advance, Jason
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
On Fri, Jun 5, 2009 at 9:54 AM, Jason Greenwald jason.greenw...@phys.chem.ethz.ch wrote: In the meantime I am using the COOT.app package from the CCP4 download site, so if anyone knows how to save more than one session using this installation, I would be happy to hear it. I couldn't find this package anywhere on the CCP4 site, so perhaps they've removed it. However, I assume that it works like any other Mac app, i.e. the actual executable is embedded somewhere in the bundle, usually in a standard place. If you're opening the program in the Finder, it will always start in your home directory. However, you can still launch the program on the command line in any directory you choose, by calling the executable itself. For instance, in MacPyMOL, /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL is the real command, and I have alias pymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL' in my .profile.
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Two more thoughts: 1. What shell are you using? if it is tcsh, then you need to source a different file, i.e., source /usr/local/xtal/coot/bin/init.csh because the syntax is not compatible with the other shells. 2. Maybe updating to the most recent X11 will help: http://xquartz.macosforge.org/trac/ Sometimes Apple's updates will clobber parts of this, and regress it to older versions of some files, which makes a mess, so if in doubt, it is always a good idea to reinstall X11. I try to compile these things with the most current X11, which might lead to incompatibilities. HTH, Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jun 5, 2009, at 9:54 AM, Jason Greenwald wrote: Thank you Bill and also other helpful folks. I should have mentioned this my original post, but when I issue the source command (which of course is also done by the coot wrapper shell script) I get the result: Illegal variable name. And coot still does not work. Perhaps something that is also of interest is that a handful of the icons are visible in the graphics window: Clear pending picks Delete item Recover session Map color Bond color Background color Preferences About and a few others. However, some others have an x icon (like for a missing image while many (the majority?) others simply have nothing to replace the missing icon. In the meantime I am using the COOT.app package from the CCP4 download site, so if anyone knows how to save more than one session using this installation, I would be happy to hear it. Cheers. Jason On Jun 5, 2009, at 6:35 PM, William G. Scott wrote: Hi Jason: For some reason that I don't understand, some users find they need to issue the command source /usr/local/xtal/coot/bin/init.sh prior to issuing the command coot (coot in this context actually invokes a wrapper shell script that has that first source command in it, so that is why I don't understand why it isn't working. If someone who is experiencing this problem feels like trying an experiment, just edit that shell script file /usr/local/xtal/coot/bin/coot and after the source line, add a line like sleep 5 before the line that invokes coot-real. I can't reproduce the problem, so I can't test this.) Sorry for the inconvenience. Bill On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg' Any ideas? Thanks in advance, Jason
