Same with me, I have Mac OS 10.11.6 (El CApitan). I couldn’t add terminal residues, then went three CCP4 updates back, it got OK, but I still can’t add OXT.
Olga > On 14 Dec 2016, at 04:51, Jobichen Chacko <[email protected]> wrote: > > 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 <[email protected]> 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.", >> <[email protected]> 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 [[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. 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 >>> >>> ------------------------------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------------------------------ >>> >>
