[phenixbb] imaginary map (anomlous difference Fourier) from phenix
Pavel Afonine
PAfonine at lbl.gov
Wed Apr 1 15:28:59 PDT 2009
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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