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
Re: [COOT] Coot and Zalman Stereo
ok, I enabled zalman stereo for gtk1 versions. This will be available from revision 2289. B *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se - Original Message - From: Paul Shaffer pshaf...@gmail.com Date: Tuesday, September 8, 2009 7:06 pm Subject: [COOT] Coot and Zalman Stereo To: COOT@JISCMAIL.AC.UK 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] Coot and Zalman Stereo
Thank you very much. I will compile and try it out when available. Cheers, Paul On Wed, Sep 9, 2009 at 11:03 AM, Bernhard Lohkamp bernhard.lohk...@ki.sewrote: ok, I enabled zalman stereo for gtk1 versions. This will be available from revision 2289. B *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se - Original Message - From: Paul Shaffer pshaf...@gmail.com Date: Tuesday, September 8, 2009 7:06 pm Subject: [COOT] Coot and Zalman Stereo To: COOT@JISCMAIL.AC.UK 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] Real space refine with hydrogens
2009/9/9 Arnaud Basle arnaud.ba...@ncl.ac.uk: Hi, I have a peptide structure at 0.92A and for the latest stage of refinement I would like to real space refine a Met residue including hydrogens. The H are flying away from their original position and density. I am using shelxl for refinement (.res and .ins format not pdb). I read from the coot mailing list archive that coot 0.4.1 was not able to do so (coot currently does not handle PDB V3 hydrogens. You need to tell reduce to write out old style hydrogens. This should take of this problem.). Is it still the case with the latest version of coot? Well, yes and no. Coot's been pdb v3 compliant for a while. This helps very little with SHELX hydrogens though, as SHELX has a different convention for H names. AFAICS, Met H atoms behave just fine (that's 0.6-pre (r2276) vs SHELX-97-2). Other H atoms, e.g. those of Leu and Ile and the like are somewhat more volatile. (The easiest is to ignore this and get them HFIXed again in the next round of shelxing). But hey, there are zillions of other reasons for upgrading to the latest Coot (and a bleeding-edge OS... hmm). JED.
