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

Dear Kevin and phenixbb readers, Clemens Vonrhein has just asked to join the BB but is not at present able to reply to past messages, so he has asked me to post this message on his behalf. Best wishes, Gerard --------------------------------------------------------------- Dear Kevin,

I note that I’ve encountered this issue with two anisotropic datasets that were ellipsoidally truncated using staraniso. This particular dataset uses a spherical cutoff, but it belongs to a student and I ran a cycle of refinement within one of my own projects that used staraniso data. May or may not be relevant, I just mention it in case an output setting is being created for the project that I don’t detect.

Your observations should not be related directly to the use of data coming out of STARANISO, i.e. subjected to cut-off by an anisotropic surface (note this it is not strictly correct to describe this cut-off as "ellipsoidal truncation") instead of a spherical/isotropic one - unless there is some special handling within phenix.refine when it encounters an input MTZ file containing an SA_flag column (that describes the signal status [1]). Or perhaps it looks at the history in the MTZ header (that might contain some information about the use of STARANISO and scaling)? There are two alternative explanations for why you now see additional map coefficients: * The MTZ file from STARANISO (if run via autoPROC [2]) might contain additional sets of amplitudes, namely F_early and F_late, that can be used not only to compute F(early)-F(late) radiation-damage detection maps [3], but also to compute normal electron-density and difference-density maps using those observed amplitudes in addition to the default ones used during refinement. * Looking at the completeness pattern, it might just be a case of the latest version now distinguishing the set of amplitudes before any outlier rejections (within refinement) and after such rejections: 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 ==> 98.14% complete amplitudes, but "only" 93.23% complete map-coefficients, i.e. maps computed /after/ outlier rejection 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 ==> 98.14% complete amplitudes, resulting in using all amplitudes before rejection (default = fill): 98.14% complete map coefficients FOFCWT_5 100.00% complete map coefficients 2FOFCWT_4 98.14% complete map coefficients 2FOFCWT_no_fill using amplitudes after rejection (default = nofill) 93.23% complete map coefficients FOFCWT_2 93.23% complete map coefficients 2FOFCWT_1 100.00% complete map coefficients 2FOFCWT_filled Does that make sense? It looks more like some rather useful provision of different ways of handling missing data (DFc completion, outlier rejection, unmeasured due to module gaps, cusp etc). It might be that anisotropic data as described by STARANISO, plus an assumption of isotropic diffraction (up to the highest diffraction limit), triggers the creation of these map coefficient variants. Does this ring a bell with developers? [1] https://staraniso.globalphasing.org/test_set_flags_about.html [2] https://www.globalphasing.com/autoproc/ [3] https://doi.org/10.1107/S2059798324001487 -- On Mon, May 20, 2024 at 03:53:01PM +0000, Dr. Kevin M Jude wrote:

Hi Billy, Here’s a dropbox linkhttps://www.dropbox.com/scl/fo/16qpqwy79pcm7zgl6j608/ADqFMcQcyUw-Jq6g-bt6LBE?rlkey=abq4uyk7oeavb0ckri9tgioek&dl=0 to input and output from one of my jobs

I note that I’ve encountered this issue with two anisotropic datasets that were ellipsoidally truncated using staraniso. This particular dataset uses a spherical cutoff, but it belongs to a student and I ran a cycle of refinement within one of my own projects that used staraniso data. May or may not be relevant, I just mention it in case an output setting is being created for the project that I don’t detect.

Best wishes Kevin

From: Billy Poon Date: Saturday, May 18, 2024 at 1:23 PM To: Elke De Zitter Cc: Dr. Kevin M Jude , phenixbb 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

On Fri, May 17, 2024 at 6:18 AM Elke De Zitter mailto:[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]> To: "phenixbb" mailto:[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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