[phenixbb] labelit.index with compatibility file

["Weiergräber, Oliver H."]

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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nicholas Sauter [nksauter at lbl.gov]
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." <o.h.weiergraeber at fz-juelich.de<mailto:o.h.weiergraeber at fz-juelich.de>> 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<tel:%2B49%202461%2061-2028>
 Fax: +49 2461 61-1448<tel:%2B49%202461%2061-1448>
================================================




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--
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Acting Head, Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratory
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