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

24 May 2024

      Dear Billy, 

Thanks for having looked into this and for working on a fix. 
I cannot reproduce this issue without modifying the output map parameters. 

Kind regards, 
Elke 

From: "Billy Poon"  
Cc: "phenixbb"  
Sent: Friday, May 24, 2024 1:05:13 AM 
Subject: Re: [phenixbb] Extra map coefficients in 1.21.1-5286 

Hi all, 
Yes, the issue is with how phenix.refine is parsing non-default output map parameters. Essentially, the defaults get reapplied and maps with the default parameters get generated. Because they have the same name, the numbers are automatically added to the name. The current workaround is to not change the map settings. We'll let you know when the fix is ready in a nightly build. We will also make a new point release with the fix. 

Let me know if you can create the issue without modifying the output map parameters. Thank you. 

-- 
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 Wed, May 22, 2024 at 12:03 AM Elke De Zitter < [ mailto:[email protected] | [email protected] ] > wrote: 

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" < [ mailto:[email protected] | [email protected] ] > 
To: "elke de-zitter" < [ mailto:[email protected] | [email protected] ] > 
Cc: "Dr. Kevin M Jude" < [ mailto:[email protected] | [email protected] ] >, "phenixbb" < [ mailto:[email protected] | [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 
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: 

BQ_BEGIN

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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BQ_END

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