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 <[log in to unmask]> 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.",
> <[log in to unmask]> 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 [[log in to unmask]]
>> Sent: Friday, December 09, 2016 4:38 PM
>> To: Weiergräber, Oliver H.
>> Cc: [log in to unmask]
>> 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."
>> <[log in to unmask]<mailto:[log in to unmask]>>
>> 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
>> [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Paul
>> Emsley [[log in to unmask]<mailto:[log in to unmask]>]
>> Sent: Friday, December 09, 2016 3:31 PM
>> To: [log in to unmask]<mailto:[log in to unmask]>
>> 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.
>>
>>
>>
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