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 Fax: +49 2461 61-9540 ================================================ ________________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Paul Emsley [[email protected]] Sent: Friday, December 09, 2016 3:31 PM To: [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. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
