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 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

...

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 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.symmetr... ? 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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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 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

...

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 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 < [email protected]> 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 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.symmetr... ? 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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_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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