Dear All, Any solution to this problem. I am also encountering this issue with MacOS, managed to revert back from the latest CCP4 update and it is working fine. Thanks. Jobi
On Sat, Dec 10, 2016 at 2:42 AM, David Waterman <dgwater...@gmail.com> wrote: > 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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