[phenixbb] symmetry rejected as inconsistent by model_vs_data

Dorothee Liebschner dcliebschner at lbl.gov
Tue Mar 29 15:22:03 PDT 2016


Hi Wolfram,

The cell dimensions are indeed within the tolerance limit. I am not sure
why they are flagged as mismatch, though.

Thanks for pointing out this case.

Best wishes,

Dorothee

On Tue, Mar 29, 2016 at 3:01 PM, wtempel <wtempel at gmail.com> wrote:

> Yes, Dorothee. It *does* work after editing the PDB file. But are not the
> two sets of cell dimensions within the tolerance limits you mentioned?
> W.
>>
> On Tue, Mar 29, 2016 at 5:31 PM, Dorothee Liebschner <dcliebschner at lbl.gov
> > wrote:
>
>> Hi Wolfram,
>>
>> Does it work with the edited pdb file?
>>
>> is_similar_symmetry is not called in model_vs_data directly, but via
>> another function. There, tolerance parameters are 1e-2 for absolute cell
>> lengths and angles.
>>
>> Best wishes,
>>
>> Dorothee
>>
>> On Tue, Mar 29, 2016 at 2:02 PM, wtempel <wtempel at gmail.com> wrote:
>>
>>> 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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>>
>
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