Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Paul just pulled off a heroic fix (rev 2310). Please try that. On Sep 11, 2009, at 7:40 AM, William G. Scott wrote: Dear Christian: I'm getting it now too. I forgot to cc you. I get it on 32-bit but not 64-bit SL. I've sent the crash report to Paul . Check to see if you have anything in ~/Library/Logs/DiagnosticReports that has coot in the title and a recent date. Bill On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote: Dear Bill, Thanks for your quick reply! I installed the new revision but it doesn't seem to make a difference (to my problems). I guess you're right and it's because I am still running 10.4 - think it's time to upgrade to 10.6, finally! Again, many thanks and best regards, Christian Am 08.09.09 16:14 schrieb William G. Scott unter wgsc...@chemistry.ucsc.edu : 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] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote: hink it's time to upgrade to 10.6, finally! 10.6.1 now. :D
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
That may be because core dump is turned off (which is default on many Linux distros). If you are using bash, try ulimit -c to see if it's the case (it'll return the maximum allowed core size). To turn it on, issue ulimit -c unlimited command. For more details, see man bash (not man ulimit as it is shell command). It only affects the current shell. HTH, Ed. On Tue, 2009-09-08 at 19:12 -0700, Engin Ozkan wrote: 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 --
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
I'm going to make a wild guess and suggest it is a python version mismatch. If you open the python scripting window and type in help() what do you see in the console window? I get this: BL INFO:: command input is: help() Welcome to Python 2.6! This is the online help utility. On Sep 8, 2009, at 10:47 AM, 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. 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
[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] 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
