Not sure whether this is closely related, but we noticed that in Coot, the SMILES option does not work in recent ccp4 versions on certain supported operating systems, specifically on CentOS 6.7 and OS X 10.11 (with both OS and ccp4 fully updated). No graphics output, the console shows different python errors:
On CentOS 6.7 with ccp4-6.5 or ccp4-7.0:
'import site' failed; use -v for traceback
Could not import runpy module
On OS X 10.11 with ccp4-7.0:
Fatal Python error: PyThreadState_Get: no current thread
Version 6.4 of ccp4 was fine on CentOS 6.x (did not test OS X), and CentOS 7 with ccp4-7.0 does not show the problem either.
Paul Emsley offers several alternative builds on the Coot home page; I found that
'coot-0.8.3-binary-Linux-x86_64-rhel-6-enhanced-ligand-gtk2-python' solves the problem for CentOS 6, while
'coot-0.8.3-binary-Linux-x86_64-rhel-6-python-gtk2' does not.
Hope that helps sort out the issue.
Best,
Oliver
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PD Dr. Oliver H. Weiergräber
Institute of Complex Systems
ICS-6: Structural Biochemistry
Tel.: +49 2461 61-2028
Fax: +49 2461 61-9540
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________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Stephen Keable [[log in to unmask]]
Sent: Sunday, April 24, 2016 9:11 AM
To: [log in to unmask]
Subject: [ccp4bb] Sketcher Problems
Dear All,
I am trying to use sketcher to create a ligand description from a ccp4 def file. I have modified an existing ligand and when I try to create a library description from the displayed structure, I encounter an error reading the file_libcheck.pdb. It seems libcheck is not running on the displayed structure and I'm not sure how to generate the restraints. Has anyone had a similar problem and know of a solution?
I'm grateful for any help.
SMK
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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
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