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"
To: "elke de-zitter"
Cc: "Dr. Kevin M Jude" , "phenixbb"
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
Web: [ https://phenix-online.org/ | https://phenix-online.org ]
On Fri, May 17, 2024 at 6:18 AM Elke De Zitter < [ mailto:[email protected] | [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" < [ mailto:[email protected] | [email protected] ] >
To: "phenixbb" < [ mailto:[email protected] | [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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