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
Fax: +49 2461 61-9540
================================================
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Paul Emsley [[log in to unmask]]
Sent: Friday, December 09, 2016 3:31 PM
To: [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.
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
|