[phenixbb] symmetry rejected as inconsistent by model_vs_data

wtempel wtempel at gmail.com
Tue Mar 29 15:01:48 PDT 2016


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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