Option to select array from mtz in phenix.real_space_refine?

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Re: [phenixbb] Highly anisotropic...

Oliver Clarke

5 Oct 2016 5 Oct '16

9:02 p.m.

Hi, I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled). However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time. Cheers Oli

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Billy Poon

5 Oct 5 Oct

9:12 p.m.

Hi Oliver, When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke wrote:

...

Hi,

I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).

However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Oliver Clarke

9:16 p.m.

New subject: Option to select array from mtz in phenix.real_space_refine?

Hi Billy, I should clarify that I typically use real_space_refine on the command line - I have not checked it in the GUI. On the command line, it provides a list of the available arrays, but no way to input a selected array (and the output of phenix.real_space_refine --help doesn’t provide any promising looking options). Cheers Oli

...

On Oct 5, 2016, at 5:12 PM, Billy Poon wrote:

Hi Oliver,

When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org https://phenix-online.org/ On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke mailto:[email protected]> wrote: Hi,

I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).

However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

Billy Poon

9:21 p.m.

Hi Oliver, Oops, the keyword for the command-line would be "map_coefficients_label". I think you have to wrap the label in quotes. Let us know if that doesn't work. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke wrote:

...

Hi Billy, I should clarify that I typically use real_space_refine on the command line - I have not checked it in the GUI.

On the command line, it provides a list of the available arrays, but no way to input a selected array (and the output of phenix.real_space_refine --help doesn’t provide any promising looking options).

Cheers Oli

On Oct 5, 2016, at 5:12 PM, Billy Poon wrote:

Hi Oliver,

When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke wrote:

...
Hi,

I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).

However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Billy Poon

9:27 p.m.

Hi Oliver, Actually, I think it's just "label" -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Oct 5, 2016 at 2:21 PM, Billy Poon wrote:

...

Hi Oliver,

Oops, the keyword for the command-line would be "map_coefficients_label". I think you have to wrap the label in quotes. Let us know if that doesn't work.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke wrote:

...
Hi Billy, I should clarify that I typically use real_space_refine on the command line - I have not checked it in the GUI.

On the command line, it provides a list of the available arrays, but no way to input a selected array (and the output of phenix.real_space_refine --help doesn’t provide any promising looking options).

Cheers Oli

On Oct 5, 2016, at 5:12 PM, Billy Poon wrote:

Hi Oliver,

When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke wrote:

...
Hi,

I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).

However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Pavel Afonine

6 Oct 6 Oct

3:07 p.m.

New subject: Option to select array from mtz in phenix.real_space_refine?

For the record: the answer is in the documentation, see https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space... -> Usage examples, #4. Pavel On 10/5/16 14:27, Billy Poon wrote:

...

Hi Oliver,

Actually, I think it's just "label"

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Oct 5, 2016 at 2:21 PM, Billy Poon mailto:[email protected]> wrote:

Hi Oliver,

Oops, the keyword for the command-line would be "map_coefficients_label". I think you have to wrap the label in quotes. Let us know if that doesn't work.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 tel:%28510%29%20486-5709 Fax: (510) 486-5909 tel:%28510%29%20486-5909 Web: https://phenix-online.org

On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke mailto:[email protected]> wrote:

Hi Billy, I should clarify that I typically use real_space_refine on the command line - I have not checked it in the GUI.

On the command line, it provides a list of the available arrays, but no way to input a selected array (and the output of phenix.real_space_refine --help doesn’t provide any promising looking options).

Cheers Oli

...
On Oct 5, 2016, at 5:12 PM, Billy Poon mailto:[email protected]> wrote:

Hi Oliver,

When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 tel:%28510%29%20486-5709 Fax: (510) 486-5909 tel:%28510%29%20486-5909 Web: https://phenix-online.org https://phenix-online.org/

On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke mailto:[email protected]> wrote:

Hi,

I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).

However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

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

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Billy Poon
Oliver Clarke
Pavel Afonine