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]> 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 > 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 > ------------------------------------------------------------ > ------------------------------------ > ------------------------------------------------------------ > ------------------------------------ >
