Dear Billy,

I don't have this behavior when running with the default settings. I encounter this issue only when I when to output non-default map coefficients (e.g. B-sharpening). When running refinement via the command-line with the "write_maps=true" keyword, I add the following map.params file:

refinement{
electron_density_maps {
    apply_default_maps = None
    map_coefficients {
      map_type = "2mFo-DFc"
      format = *mtz phs
      mtz_label_amplitudes = "2FOFCWT"
      mtz_label_phases = "PH2FOFCWT"
      fill_missing_f_obs = True
      sharpening = True
      sharpening_b_factor = None
    }
    map_coefficients {
      map_type = "2mFo-DFc"
      format = *mtz phs
      mtz_label_amplitudes = "2FOFCWT_no_fill"
      mtz_label_phases = "PH2FOFCWT_no_fill"
      fill_missing_f_obs = False
      sharpening = True
      sharpening_b_factor = None
    }
    map_coefficients {
      map_type = "mFo-DFc"
      format = *mtz phs
      mtz_label_amplitudes = "FOFCWT"
      mtz_label_phases = "PHFOFCWT"
      fill_missing_f_obs = False
      sharpening = False
      sharpening_b_factor = None
    }
    map {
      map_type = "2mFo-DFc"
      format = xplor *ccp4
      file_name = None
      fill_missing_f_obs = True
      sharpening = True
      sharpening_b_factor = None
    }
    map {
      map_type = "2mFo-DFc"
      format = xplor *ccp4
      file_name = None
      fill_missing_f_obs = False
      sharpening = True
      sharpening_b_factor = None
    }
    map {
      map_type = "mFo-DFc"
      format = xplor *ccp4
      file_name = None
      fill_missing_f_obs = False
      sharpening = False
      sharpening_b_factor = None
    }
}
}

The mtz files I use have different types of column labels, hence I don't think it has to do with the input file. I can share files off-list if you wish.

All the best
Elke

From: "Billy Poon" <[email protected]>
To: "elke de-zitter" <[email protected]>
Cc: "Dr. Kevin M Jude" <[email protected]>, "phenixbb" <[email protected]>
Sent: Saturday, May 18, 2024 10:22:59 PM
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


On Fri, May 17, 2024 at 6:18 AM Elke De Zitter <[email protected]> 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

From: "Dr. Kevin M Jude" <[email protected]>
To: "phenixbb" <[email protected]>
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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