[phenixbb] symmetry rejected as inconsistent by model_vs_data

wtempel wtempel at gmail.com
Tue Mar 29 14:02:23 PDT 2016


Hello Dorothee,
the "mismatch" flag did indeed lead me to edit the PDB's cell dimensions
and model_vs_data runs.
With which tolerance parameters does model_vs_data call
is_similar_symmetry? Tighter than the defaults listed in the documentation?
Regards,
Wolfram

On Tue, Mar 29, 2016 at 4:43 PM, Dorothee Liebschner <dcliebschner at lbl.gov>
wrote:

> Hi Wolfram,
>
> Yes, this is correct. The machinery used to read in the files uses
> is_similar_symmetry to check for symmetry mismatch.
> As it is on a deeper level than model_vs_data, there is no keyword to
> override this, unfortunately.
>
> In your example, did you try to edit your pdb file so that the unit cell
> dimensions match exactly?
>
> Best wishes,
>
> Dorothee
>
> On Tue, Mar 29, 2016 at 12:47 PM, wtempel <wtempel at gmail.com> wrote:
>
>> Hello,
>> phenix.model_vs_data_1.10.1-2155,
>> along with printing to stderr:
>> Sorry: Crystal symmetry mismatch between different files.
>>
>> prints these, and only these, lines to stdout:
>>
>>
>> x251682_scaled3.mtz (36.692, 53.798, 108.063, 90, 84.258, 90) P 1 21 1
>> readySet.pdb (36.69, 53.8, 108.06, 90, 84.26, 90) P 1 21 1
>>
>>
>> Is this related to this code
>> <http://cci.lbl.gov/cctbx_docs/cctbx/cctbx.crystal.html#cctbx.crystal.symmetry.is_similar_symmetry>
>> ?
>> Can I force phenix.model_vs_data to omit this isomorphism check and “run”
>> with the reflection dimensions?
>> Thank you.
>> Wolfram
>>>>
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>
>
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