Dear Oliver, Thanks for digging deeper. I don't know why this should matter either, but now we should be able to investigate further.
Cheers David On Fri, 9 Dec 2016, 18:03 "Weiergräber, Oliver H.", < o.h.weiergrae...@fz-juelich.de> wrote: > 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 [dgwater...@gmail.com] > Sent: Friday, December 09, 2016 4:38 PM > To: Weiergräber, Oliver H. > Cc: CCP4BB@jiscmail.ac.uk > 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." < > o.h.weiergrae...@fz-juelich.de<mailto:o.h.weiergrae...@fz-juelich.de>> > 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 [CCP4BB@JISCMAIL.AC.UK<mailto: > CCP4BB@JISCMAIL.AC.UK>] on behalf of Paul Emsley [ > pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>] > Sent: Friday, December 09, 2016 3:31 PM > To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > 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. 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