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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