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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