Hi Volks, thanks for this discussion. It helped me in finding coot 0.5 for 10.4 and installing it. However the last step described below was not quite the last one to make coot running (at least for me). Running command line launching /Applications/coot.app/Contents/MacOS/coot would give me the error message: --------------------------------------------------- ...
~/.coot-preferences/coot-preferences.scm:5:1: In expression (set-file-chooser-selector 0): ~/.coot-preferences/coot-preferences.scm:5:1: Unbound variable: set-file-chooser-selector coot-exe: "/Applications/coot.app/Contents/MacOS/../coot/bin/coot" coot-version: /Applications/coot.app/Contents/MacOS/../coot/bin/coot core: #f No core file found. No debugging --------------------------------------------------- So I tried to delete ~/.coot-preferences/coot-preferences.scm and that finally worked. HTH, mkl ________________________________ Da: Abhinav Kumar <[EMAIL PROTECTED]> A: [email protected] Inviato: Venerdì 21 novembre 2008, 3:10:55 Oggetto: Re: Updating coot on Mac OS X 10.4 Hi Charles, This worked fine. Wonderful. Thanks so much. I guess what was left unspecified was the path to the coot binary, i.e. /Applications/coot.app/Contents/MacOS/coot Iain, please try this out. Thanks Abhinav Abhinav Kumar JCSG @ SSRL, MS 99 2575 Sand Hill Road Menlo Park, CA 945025-7015 Phone: 650 926 2992 Fax: 650 926 3292 On Nov 20, 2008, at 12:45 AM, Ballard, CC ((Charles)) wrote: Hi can you command line launch using /Applications/coot.app/Contents/MacOS/coot that runs a setup script that sets the environment Charles ________________________________ From: Abhinav Kumar [mailto:[EMAIL PROTECTED] Sent: 19 November 2008 23:09 To: Ballard, CC (Charles) Subject: Re: [COOT] Updating coot on Mac OS X 10.4 Thanks Charles. Where do I find the crash log? I didn't use a terminal to start coot, rather, used mouse to click on coot icon in Application folder. However, I also tried running coot from /Applications/coot.app/Content/coot/bin/coot and got this: ======================================================== If have found this software to be useful, you are requested to cite: Coot: model-building tools for molecular graphics Emsley P, Cowtan K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004 The reference for the REFMAC5 Dictionary is: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, Murshudov GN ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004 If using "SSM Superposition", please cite: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel E, Henrick K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004 Acquiring application resources from //Users/Shared/pac5/coot/coot.app/Contents/coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir //Users/Shared/pac5/coot/coot.app/Contents/coot/share/coot/pixmaps ** (coot:15026): WARNING **: Couldn't find pixmap file: coot-0.5.xpm (coot:15026): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/Users/Shared/pac6/coot/coot.app/Contents/coot/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (coot:15026): GdkPixbuf-WARNING **: Error loading XPM image loader: Image type 'xpm' is not supported ** ERROR **: Couldn't create replacement pixmap. aborting... Abort ========================================================================== Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Ballard, CC (Charles) wrote: Hi Abhinav I am responsible for the failed binary. Can you send me the crash log from console.app ? As soon as CCP4 6.1 is out of the door (possibly even by this Friday) I will take a look at it. Charles Ballard CCP4 -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Abhinav Kumar Sent: 19 November 2008 20:04 To: [email protected] Subject: Re: [COOT] Updating coot on Mac OS X 10.4 Thanks Iain. I downloaded the package and it installed without any problem. However, when I click on it to start, it pop ups the starting logo and then disappears. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Iain Kerr wrote: I was pointed to a universal installer here: http://www.ccp4.ac.uk/download/os.php Didn't work for me though..perhaps it will work on your system. HTH, Iain Abhinav Kumar wrote: Hi Paul and Bill, I have a Mac OS X 10.4 (tiger). I wanted to update coot to the latest version. Since Bill's old machine (10.4) died, there is no instruction for updating coot to 0.5 version. Is there some way of doing it. I have had problems using fink to update it.
