imaginary map (anomlous difference Fourier) from phenix
Hi everybody, I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me, Ulrich # source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152) The mapcoeff.mtz looks like OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM No. of reflections used in FILE STATISTICS 72570 1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16
Hi Ulrich, sorry for delayed reply. I just checked this myself with the latest version. Here is my favorite test case: http://cci.lbl.gov/~afonine/lysozime_gold/ The files are: data.mtz - file with Fobs lysozyme.pdb - best refined model that included gold (Au) lysozyme_poor_noAU.pdb - unrefined model without Au maps_001_map_coeffs.mtz - map coefficients file run - file with phenix.refine command To test if phenix.refine produces the correct anomalous difference map coefficients, I ran this command ("run" file): phenix.refine data.mtz lysozyme_poor_noAU.pdb strategy=none main.number_of_mac=1 --overwrite output.prefix=maps this does not do any refinement but computes maps only. Use "phenix.mtz.dump maps_001_map_coeffs.mtz" to see the content of maps_001_map_coeffs.mtz file. Now, if I load in COOT the map coefficients file (maps_001_map_coeffs.mtz, result of the above run) (labels ANOM,PHANOM) and the model (lysozyme.pdb, best refined model), and center on Au, I see very strong density peak (see a screen-shot picture: Au_density.png). So, this shows me that the option works well... I'm not sure what happens in your case. This map (ANOM,PHANOM) is computed automatically if your input datafile contains Fobs(+) and Fobs(-), so you don't need to use any special command for this. If you want me to have a look, please send me the data and model files (along with anom. sites) and I will check it myself. Pavel. On 3/31/09 9:18 AM, Ulrich Baumann wrote:
Hi everybody,
I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me,
Ulrich
# source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152)
The mapcoeff.mtz looks like
OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 =======================
Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label
1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM
No. of reflections used in FILE STATISTICS 72570
1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16 ------------------------------------------------------------------------
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Hi Ulrich, there was a bug in phenix.refine that was causing this behavior. The bug is fixed now. Please use the most recent development version of PHENIX (made after April 3): https://www.phenix-online.org/download/phenix/nightly/ Pavel. On 3/31/09 9:18 AM, Ulrich Baumann wrote:
Hi everybody,
I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me,
Ulrich
# source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152)
The mapcoeff.mtz looks like
OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 =======================
Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label
1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM
No. of reflections used in FILE STATISTICS 72570
1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16 ------------------------------------------------------------------------
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participants (2)
-
Pavel Afonine -
Ulrich Baumann