Re: [phenixbb] Extra map coefficients in 1.21.1-5286

Hi Billy, To add to Kevin's point, we observed this recently also with Staraniso-processed data. So, one more data point supporting that. Should have reported it earlier. Thank you for the fantastic software, Engin On 5/20/24 10:53 AM, Dr. Kevin M Jude wrote:

Hi Billy,

Here’s a dropbox link https://www.dropbox.com/scl/fo/16qpqwy79pcm7zgl6j608/ADqFMcQcyUw-Jq6g-bt6LBE?rlkey=abq4uyk7oeavb0ckri9tgioek&dl=0 to input and output from one of my jobs

I note that I’ve encountered this issue with two anisotropic datasets that were ellipsoidally truncated using staraniso. This particular dataset uses a spherical cutoff, but it belongs to a student and I ran a cycle of refinement within one of my own projects that used staraniso data. May or may not be relevant, I just mention it in case an output setting is being created for the project that I don’t detect.

Best wishes

Kevin

*From: *Billy Poon *Date: *Saturday, May 18, 2024 at 1:23 PM *To: *Elke De Zitter *Cc: *Dr. Kevin M Jude , phenixbb *Subject: *Re: [phenixbb] Extra map coefficients in 1.21.1-5286

Dear Kevin and Elke,

Can you provide your input files and settings so that we can reproduce the issue? The settings are available from the "Results" tab with the "Config file" button. Alternatively, the settings are available by selecting the job in your job history and clicking the "Show details" button. A dialog will pop up and show the location of the job and the config file. I am not able to get the numbered map coefficients with a tutorial dataset with default settings. Thanks!

--

Billy K. Poon

Research Scientist, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory

1 Cyclotron Road, M/S 33R0345

Berkeley, CA 94720

Fax: (510) 486-5909

Web: https://phenix-online.org

On Fri, May 17, 2024 at 6:18 AM Elke De Zitter wrote:

Dear Kevin,

I am facing the same problem upon running phenix.refine 1.21 from the command line with a map.params input file or via the GUI when the default map behavior is altered (e.g. B-sharpening). In phenix.refine 1.20, the new map coefficient parameters would replace the default ones. I have the impression that in phenix.refine 1.21 the new map coefficient parameters add up to the defaults, leading to many additional columns. I find it confusing as well since I have to figure out myself which coefficients are stored in *_1 etc. And, as you pointed out these mtz column labels are not automatically recognized.

It would be nice to have a workaround and get the same output as when using phenix 1.20. I couldn't find one (except for using version 1.20). Suggestions are thus welcome :-)

In case it is relevant, I am running phenix on a Mac. I tried version 1.21.1-5286 and dev-5330.

Kind regards,

Elke

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*From: *"Dr. Kevin M Jude" *To: *"phenixbb" *Sent: *Thursday, May 2, 2024 5:52:56 PM *Subject: *[phenixbb] Extra map coefficients in 1.21.1-5286

In my latest installed version of phenix, I find that additional, redundant map coefficients are being added to the output mtz file. I compare an identical refinement originally run in 1.21rc1_5058 and then repeated in 1.21.1-5286. *_filled and *_4 appear to be redundant, and the final sets of coefficients (*_no_fill and *_5), appear to include the test set reflections, even though I’ve selected Exclude R-free set from map coefficients in the gui. This is a little bit confusing, but primarily an annoyance because auto-open mtz in coot can’t figure out which coefficients to use.

1.21rc1_5058

Col Sort Min    Max    Num      %     Mean Mean   Resolution   Type Column

num order               Missing complete          abs.   Low High       label

   1 NONE -42      41      0  100.00     -3.3 16.0  52.38   1.96   H  H

   2 NONE 0      28      0  100.00     10.3 10.3  52.38   1.96   H  K

   3 NONE 0      27      0  100.00     10.3 10.3  52.38   1.96   H  L

   4 NONE  -94.4 13012.5   269   98.44    85.01    85.49 45.63   1.96   J  I-obs

   5 NONE 0.2   337.4   269   98.44     4.44 4.44  45.63   1.96   Q  SIGI-obs

   6 NONE 0.0     1.0   269   98.44     0.05 0.05  45.63   1.96   I  R-free-flags

   7 NONE 10.2  2509.6   321   98.14   129.94 129.94  36.90   1.96   F  F-obs-filtered

   8 NONE 1.3    35.8   321   98.14    10.11 10.11  36.90   1.96   Q SIGF-obs-filtered

   9 NONE 0.1  2250.2   321   98.14   125.18 125.18  36.90   1.96   F  F-model

  10 NONE -180.0   180.0   321   98.14     4.35 89.81  36.90   1.96   P  PHIF-model

  11 NONE 0.0  2971.8  1165   93.23   117.81 117.81  36.90   1.96   F  2FOFCWT

  12 NONE -180.0   180.0  1165   93.23     4.65 89.89  36.90   1.96   P  PH2FOFCWT

  13 NONE 0.0  2971.8     0  100.00   117.93 117.93  52.38   1.96   F  2FOFCWT_filled

  14 NONE -180.0   180.0     0  100.00     4.85 90.05  52.38   1.96   P PH2FOFCWT_filled

  15 NONE 0.0   738.9  1165   93.23    46.86 46.86  36.90   1.96   F  FOFCWT

  16 NONE -180.0   180.0  1165   93.23     4.75 90.35  36.90   1.96   P  PHFOFCWT

1.21.1-5286

Col Sort Min    Max    Num      %     Mean Mean   Resolution   Type Column

num order               Missing complete          abs.   Low High       label

   1 NONE -42      41      0  100.00     -3.3 16.0  52.38   1.96   H  H

   2 NONE 0      28      0  100.00     10.3 10.3  52.38   1.96   H  K

   3 NONE 0      27      0  100.00     10.3 10.3  52.38   1.96   H  L

   4 NONE  -94.4 13012.5   269   98.44    85.01    85.49 45.63   1.96   J  I-obs

   5 NONE 0.2   337.4   269   98.44     4.44 4.44  45.63   1.96   Q  SIGI-obs

   6 NONE 0.0     1.0   269   98.44     0.05 0.05  45.63   1.96   I  R-free-flags

   7 NONE 10.3  2535.0   321   98.14   131.25 131.25  36.90   1.96   F  F-obs-filtered

   8 NONE 1.3    36.1   321   98.14    10.21 10.21  36.90   1.96   Q SIGF-obs-filtered

   9 NONE 0.0  2261.4   321   98.14   126.66 126.66  36.90   1.96   F  F-model

  10 NONE -180.0   180.0   321   98.14     3.96 89.82  36.90   1.96   P  PHIF-model

  11 NONE 0.0  3119.6  1165   93.23   119.71 119.71  36.90   1.96   F  2FOFCWT_1

  12 NONE -180.0   180.0  1165   93.23     4.33 89.89  36.90   1.96   P  PH2FOFCWT_1

  13 NONE 0.0  3119.6     0  100.00   119.85 119.85  52.38   1.96   F  2FOFCWT_filled

  14 NONE -180.0   180.0     0  100.00     4.44 90.05  52.38   1.96   P PH2FOFCWT_filled

  15 NONE 0.0   780.4  1165   93.23    45.28 45.28  36.90   1.96   F  FOFCWT_2

  16 NONE -180.0   180.0  1165   93.23     4.21 90.36  36.90   1.96   P  PHFOFCWT_2

  17 NONE 0.0  3119.6     0  100.00   119.74 119.74  52.38   1.96   F  2FOFCWT_4

  18 NONE -180.0   180.0     0  100.00     4.60 90.01  52.38   1.96   P  PH2FOFCWT_4

  19 NONE 0.0  3119.6   321   98.14   119.56 119.56  36.90   1.96   F 2FOFCWT_no_fill

  20 NONE -180.0   180.0   321   98.14     4.40 89.94  36.90   1.96   P PH2FOFCWT_no_fill

  21 NONE 0.0   780.4   321   98.14    45.68 45.68  36.90   1.96   F  FOFCWT_5

  22 NONE -180.0   180.0   321   98.14     4.12 90.23  36.90   1.96   P  PHFOFCWT_5

Best wishes

Kevin

--

Kevin Jude, PhD

Structural Biology Research Specialist, Garcia Lab

Howard Hughes Medical Institute

Stanford University School of Medicine

Beckman B177, 279 Campus Drive, Stanford CA 94305

Phone: (650) 723-6431

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-- Engin Özkan, Ph.D. Associate Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu