[phenixbb] symmetry rejected as inconsistent by model_vs_data

[Dorothee Liebschner]

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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