[phenixbb] labelit.index with compatibility file

Nicholas Sauter nksauter at lbl.gov
Fri Apr 20 08:39:28 PDT 2012


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." <
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
>  Fax: +49 2461 61-1448
> ================================================
>
>
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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
1 Cyclotron Rd., Bldg. 64R0121
Berkeley, CA 94720-8118
(510) 486-5713
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