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"
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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