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Plots of local real-space CC

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Murpholino Peligro

27 Feb 2018 27 Feb '18

5:04 p.m.

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that? I want to plot those values with gnuplot. I do not want the whole graph (red and green lines). Thanks Murphy

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Billy Poon

27 Feb 27 Feb

5:22 p.m.

Hi Murphy, Near table below the "Multi-criterion plot" button, you can click "Save all results to file" to create a comma-separated text file with all the numbers for the graphs. You can then extract the CC values with a spreadsheet or some other parsing method. Let us know of any other questions. 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 Tue, Feb 27, 2018 at 9:04 AM, Murpholino Peligro wrote:

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that?

I want to plot those values with gnuplot. I do not want the whole graph (red and green lines).

Thanks

Murphy

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Edwin Pozharski

5:25 p.m.

There may be reasons why you prefer molprobity output, but why not use phenix.real_space_correlation or phenix.model_vs_data? On Tue, Feb 27, 2018 at 12:04 PM, Murpholino Peligro wrote:

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that?

I want to plot those values with gnuplot. I do not want the whole graph (red and green lines).

Thanks

Murphy

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Murpholino Peligro

5:42 p.m.

Thanks BP. That's exactly what I want. EP: I tried phenix.real_space_correlation at the cli, but it gives values per atom not per residue. 2018-02-27 11:25 GMT-06:00 Edwin Pozharski :

There may be reasons why you prefer molprobity output, but why not use phenix.real_space_correlation or phenix.model_vs_data?

On Tue, Feb 27, 2018 at 12:04 PM, Murpholino Peligro < [email protected]> wrote:

...
Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that?

I want to plot those values with gnuplot. I do not want the whole graph (red and green lines).

Thanks

Murphy

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Edwin Pozharski

6:40 p.m.

Add detail="residue" to your command and it calculates CC per residue. On Tue, Feb 27, 2018 at 12:42 PM, Murpholino Peligro wrote:

Thanks BP. That's exactly what I want. EP: I tried phenix.real_space_correlation at the cli, but it gives values per atom not per residue.

2018-02-27 11:25 GMT-06:00 Edwin Pozharski :

...
There may be reasons why you prefer molprobity output, but why not use phenix.real_space_correlation or phenix.model_vs_data?

On Tue, Feb 27, 2018 at 12:04 PM, Murpholino Peligro < [email protected]> wrote:

...
Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that?

I want to plot those values with gnuplot. I do not want the whole graph (red and green lines).

Thanks

Murphy

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Murpholino Peligro

8:08 p.m.

Thanks EP ...now ...that's really exactly what I want. 2018-02-27 12:40 GMT-06:00 Edwin Pozharski :

Add detail="residue" to your command and it calculates CC per residue.

On Tue, Feb 27, 2018 at 12:42 PM, Murpholino Peligro < [email protected]> wrote:

...
Thanks BP. That's exactly what I want. EP: I tried phenix.real_space_correlation at the cli, but it gives values per atom not per residue.

2018-02-27 11:25 GMT-06:00 Edwin Pozharski :

...
There may be reasons why you prefer molprobity output, but why not use phenix.real_space_correlation or phenix.model_vs_data?

On Tue, Feb 27, 2018 at 12:04 PM, Murpholino Peligro < [email protected]> wrote:

...
Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that?

I want to plot those values with gnuplot. I do not want the whole graph (red and green lines).

Thanks

Murphy

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Billy Poon
Edwin Pozharski
Murpholino Peligro