Dear David, well, 1D2F does cause the issue for me, or at least it _did_ until I found the real issue.
In fact, I could not reproduce the problem on a second machine, so I started testing for problems with my user environment (by cleaning up my shell start-up file to the bare minimum, deleting .coot-preferences etc.), but to no avail. What finally turned out to be responsible was a tiny modification to the system-wide environment: I had recently added /usr/lib64/gtk-2.0/modules to the ld.so.conf path in order to expose these (default) libraries to third-party programs that would not otherwise find them. After removing this path, geometry analysis in coot started working again. But it's really hard to understand how these libraries should be harmful to the operation of coot, and specifically prevent it from properly handling OXT atoms. And all this did not affect Paul's version... Anyway, thanks a lot for looking into this Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ________________________________________ From: David Waterman [[email protected]] Sent: Friday, December 09, 2016 4:38 PM To: Weiergräber, Oliver H. Cc: [email protected] Subject: Re: [ccp4bb] Bug in latest COOT Dear Oliver, I just tried this on 1D2F using computers at Diamond (Red Hat Enterprise Linux Workstation release 6.8 (Santiago)) with coot in CCP4 7.0.025 and all was well. Could you send me, or point me towards, a PDB that causes the issue - and exact instructions for how to trigger it? Cheers -- David On 9 December 2016 at 14:59, "Weiergräber, Oliver H." <[email protected]<mailto:[email protected]>> wrote: Hello Paul and ccp4 devs, as I mentioned, the crashing coot version is the one provided with the latest ccp4 update(s), i.e. --------------------------------------- 0.8.7 (revision-count 6498) [with guile 1.8.8 embedded] [with python 2.7.10 embedded] Binary type: Linux-x86_64-centos-5-python-gtk2 Builder_info: CCP4, Oxfordshire --------------------------------------- Running CentOS 6.8 here, but any EL6 incarnation should behave in the same way. This is the console output after invoking geometry analysis: --------------------------------------- Unknown element :: /usr/local/ccp4-7.0/bin/coot: line 284: 17416 Segmentation fault (core dumped) $coot_bin "$@" coot-exe: "/usr/local/ccp4-7.0/libexec/coot-bin" coot-version: /usr/local/ccp4-7.0/libexec/coot-bin platform: /bin/uname core: #f No core file found. No debugging --------------------------------------- Line 284 is just the final fi statement, without obvious (to me at least) relation to geometry analysis ... Hope this helps Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028<tel:%2B49%202461%2061-2028> Fax: +49 2461 61-9540<tel:%2B49%202461%2061-9540> ================================================ ________________________________________ From: CCP4 bulletin board [[email protected]<mailto:[email protected]>] on behalf of Paul Emsley [[email protected]<mailto:[email protected]>] Sent: Friday, December 09, 2016 3:31 PM To: [email protected]<mailto:[email protected]> Subject: Re: [ccp4bb] Bug in latest COOT On 09/12/16 14:13, "Weiergräber, Oliver H." wrote: > Hello, > > after installing the latest ccp4 updates today, I found that coot will > consistently crash (core dump) if geometry analysis is run on _any_ structure > containing an OXT atom. > > Hello Oliver, When reporting a bug you should try to include as much information as possible so that the developer can reproduce it. Ideally include a backtrace, but at the minimum you should include the operating system and version of coot that you are using: $ coot --version-full Having said that, I don't really follow what CCP4 do to Coot before they distribute the binaries. Official coot binaries are tested before publication - so I'd recommend you use those. It goes without saying that I can't reproduce the problem that you mentioned - and even CCP4's build of Coot 0.8.7 (on Macintosh 10.10) seems not to have this problem. http://www.chiark.greenend.org.uk/~sgtatham/bugs.html Paul. ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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