Hello, I have used labelit.check_pdb_symmetry to evaluate a P1 dataset and model for possible higher symmetry. C2 turned out to be a candidate solution. When I used the new asymmetric unit content file (xyz_coset0.pdb) to force indexing in the new SG: labelit.index /path/to/my/images/template_####.img 1 90 compatibility_file=xyz_coset0.pdb, the program crashes with AttributeError: 'NoneType' object has no attribute 'mosaicity_spot_coverage' This happens with the version included in phenix-1.7.3 as well as with the latest standalone labelit package. Any ideas what might be causing this? Maybe the new cell fails to refine? It is absolutely possible that forcing the higher symmetry SG leads to significant positional rmsd - I actually believe that P1 is correct, but it's definitly not far from C2. Best regards ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app
Oliver, I'll have a look at this and possibly contact you for additional information offline. Nick Sauter On Fri, Apr 20, 2012 at 1:50 AM, "Weiergräber, Oliver H." < [email protected]> wrote:
Hello,
I have used labelit.check_pdb_symmetry to evaluate a P1 dataset and model for possible higher symmetry. C2 turned out to be a candidate solution. When I used the new asymmetric unit content file (xyz_coset0.pdb) to force indexing in the new SG: labelit.index /path/to/my/images/template_####.img 1 90 compatibility_file=xyz_coset0.pdb, the program crashes with
AttributeError: 'NoneType' object has no attribute 'mosaicity_spot_coverage'
This happens with the version included in phenix-1.7.3 as well as with the latest standalone labelit package.
Any ideas what might be causing this? Maybe the new cell fails to refine? It is absolutely possible that forcing the higher symmetry SG leads to significant positional rmsd - I actually believe that P1 is correct, but it's definitly not far from C2.
Best regards
================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================
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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. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
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------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Acting Head, Berkeley Center for Structural Biology Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713
Oliver, The bug has been fixed. The fixes will appear in the next nightly PHENIX build (dev-1043 or higher). Nick On Fri, Apr 20, 2012 at 1:50 AM, "Weiergräber, Oliver H." < [email protected]> wrote:
Hello,
I have used labelit.check_pdb_symmetry to evaluate a P1 dataset and model for possible higher symmetry. C2 turned out to be a candidate solution. When I used the new asymmetric unit content file (xyz_coset0.pdb) to force indexing in the new SG: labelit.index /path/to/my/images/template_####.img 1 90 compatibility_file=xyz_coset0.pdb, the program crashes with
AttributeError: 'NoneType' object has no attribute 'mosaicity_spot_coverage'
This happens with the version included in phenix-1.7.3 as well as with the latest standalone labelit package.
Any ideas what might be causing this? Maybe the new cell fails to refine? It is absolutely possible that forcing the higher symmetry SG leads to significant positional rmsd - I actually believe that P1 is correct, but it's definitly not far from C2.
Best regards
================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------ 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. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Acting Head, Berkeley Center for Structural Biology Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713
Hello Nick,
thanks a lot for your efforts.
Best regards,
Oliver
================================================
PD Dr. Oliver H. Weiergräber
Institute of Complex Systems
ICS-6: Structural Biochemistry
Tel.: +49 2461 61-2028
Fax: +49 2461 61-1448
================================================
________________________________________
From: [email protected] [[email protected]] on behalf of Nicholas Sauter [[email protected]]
Sent: Tuesday, April 24, 2012 12:20 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] labelit.index with compatibility file
Oliver,
The bug has been fixed. The fixes will appear in the next nightly PHENIX build (dev-1043 or higher).
Nick
On Fri, Apr 20, 2012 at 1:50 AM, "Weiergräber, Oliver H."
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