[COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Hi Christian: I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a bug on 64-bit where the menu would freeze when superposition is invoked. I suppose there is a 0.001 chance that it fixes the other problem too. I have no way to test on 10.5 intel (I still have 10.6) and haven't had direct access to 10.4 for a long time. This could be a problem with coot or with one of many of its ca. 230 dependencies. From what I have read, you can upgrade directly to SL (US $30, UK £25), despite the propaganda on the box. I have ccp4 and coot and the other crystallographic fink things running all in 64-bit now. I'm hoping these will now pass the 70S ribosome test. I hope this works in the meantime. Bill On Sep 8, 2009, at 5:08 AM, Christian Benda wrote: Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de
Re: [COOT] Coot osx 10.6 problem
The good news is I can reproduce your error: checking for GtkGLExt - version = 1.0.0... no *** Could not run GtkGLExt test program, checking why... *** The test program failed to compile or link. See the file config.log for the *** exact error that occured. This usually means GtkGLExt is incorrectly installed. ### execution of /var/tmp/tmp.2.JleDIx failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2283-1 (Reading database ... 201033 files and directories currently installed.) I'm coming to the conclusion that upgrading 32-bit fink to SL on a 64- bit capable machine is more trouble than a fresh install of 64-bit fink. I'll try to get this sorted out. Sorry. Bill On Sep 8, 2009, at 7:30 AM, Dima Chirgadze wrote: Dear Bill, I am having problems installing latest version of coot under snow leopard. 1) I have installed fink 0.29.9 (32-bit) via bootstrapping on a Snow Leopard machine. 2) changed the /sw/etc/fink.conf according to your website and updated fink 3) changed /sw/etc/apt/sources.list to include deb http://sage.ucsc.edu/fink_intel_10.6_32bit stable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_32bit unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_32bit local main 4) when I do: fink -b install coot, it installs/updates about 100 packages and then I get the following error: --snip-- checking for pkg-config... (cached) /sw/bin/pkg-config checking for GtkGLExt - version = 1.0.0... no *** Could not run GtkGLExt test program, checking why... *** The test program failed to compile or link. See the file config.log for the *** exact error that occured. This usually means GtkGLExt is incorrectly installed. ### execution of /var/tmp/tmp.2.MhYZKK failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2265-1 (Reading database ... 25946 files and directories currently installed.) Removing fink-buildlock-coot-0.6-pre-1-revision-2265-1 ... Failed: phase compiling: coot-0.6-pre-1-revision-2265-1 failed --snip-- I've searched the lists but couldn't get it working I tried re-installing gtkglext1 and gtkglext1-shlibs. The $LD_LIBRARY_PATH and/or $DYLD_LIBRARY_PATH both are unset. I still cannot install. Could you please help me to resolve it? Thank you very much in advance, Regards, Dima Dimitri (aka Dima) Chirgadze, PhD Senior Research Associate Department of Biochemistry University of Cambridge Cambridge, CB2 1GA UK Tel: +44 1223 766029 Fax: +44 1223 766082
Re: [COOT] Coot and Zalman Stereo
Be careful how you look at it. As far as I can from trying it here, the stereo effect is very critically dependent on the vertical position of your eyes relative to the screen normal (or screen tilt if you like). Try tilting the screen Phil On 8 Sep 2009, at 17:55, Paul Shaffer wrote: Hi All, I recently acquired a Zalman 3D 22inch monitor with much anticipation. However, building the latest pre-release of Coot and invoking zalman stereo mode, it did not work. There are two images being displayed, but they are both displayed on all 1050 lines rather than alterating even and odd lines to give the left and right eye images. What I believe to be the relevant facts are these, the OS is RHEL3 with the latest nVidia linux drivers and coot version 2283 built using the auto-building script for a gtk1 build with python both enabled or disabled. The log files from compiling coot and the numerous dependancies looks ok without any obivous errors. Any suggestions? Is this a product of an outdated OS? Thanks in advance, Paul
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Hi everybody, Using the revision 2283 on 10.5, I am seeing this whenever I am closing the application: /sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-real $@ Yep, coot shuts down with a segmentation fault. I haven't tested most functionality and it has not affected my use of coot yet, but I assumed it might help to report it. This seems to be the same bug observed by Christian on a 10.4 machine, because I get the similar Preferences crash. Empty 0-coot.state.scm is also probably due to the crash during exiting. Engin On 9/8/09 7:14 AM, William G. Scott wrote: Hi Christian: I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a bug on 64-bit where the menu would freeze when superposition is invoked. I suppose there is a 0.001 chance that it fixes the other problem too. I have no way to test on 10.5 intel (I still have 10.6) and haven't had direct access to 10.4 for a long time. This could be a problem with coot or with one of many of its ca. 230 dependencies. From what I have read, you can upgrade directly to SL (US $30, UK £25), despite the propaganda on the box. I have ccp4 and coot and the other crystallographic fink things running all in 64-bit now. I'm hoping these will now pass the 70S ribosome test. I hope this works in the meantime. Bill On Sep 8, 2009, at 5:08 AM, Christian Benda wrote: Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Engin Ozkan wrote: Hi everybody, Using the revision 2283 on 10.5, I am seeing this whenever I am closing the application: /sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-real $@ Yep, coot shuts down with a segmentation fault. I haven't tested most functionality and it has not affected my use of coot yet, but I assumed it might help to report it. This seems to be the same bug observed by Christian on a 10.4 machine, because I get the similar Preferences crash. Empty 0-coot.state.scm is also probably due to the crash during exiting. Dear MacCoot-bug-finders, It would be very useful (making the difference between a bug being probably not fixable to probably fixable) if you could send me the core dump analysis of coot. Coot will leave a core dump in /cores - at least it does for me (look for the latest one) $ gdb /sw/bin/coot-real /cores/cores. where send me that text output. Thanks, Paul
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
That is actually a very reasonable request. Sorry for missing that. However, this bug does not leave any core dumps anywhere I could find, including in /cores. Engin On 9/8/09 10:58 AM, Paul Emsley wrote: Engin Ozkan wrote: Hi everybody, Using the revision 2283 on 10.5, I am seeing this whenever I am closing the application: /sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-real $@ Yep, coot shuts down with a segmentation fault. I haven't tested most functionality and it has not affected my use of coot yet, but I assumed it might help to report it. This seems to be the same bug observed by Christian on a 10.4 machine, because I get the similar Preferences crash. Empty 0-coot.state.scm is also probably due to the crash during exiting. Dear MacCoot-bug-finders, It would be very useful (making the difference between a bug being probably not fixable to probably fixable) if you could send me the core dump analysis of coot. Coot will leave a core dump in /cores - at least it does for me (look for the latest one) $ gdb /sw/bin/coot-real /cores/cores. where send me that text output. Thanks, Paul -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
