[phenixbb] reflection files, anomalous data, and test set
Mark Collins
mcollins at convex.hhmi.columbia.edu
Wed Jul 23 15:39:26 PDT 2008
Hello again,
I'm still seem to have a problem with merging these files.
I tried this in my .params file but phenix can't use my test set, any
suggestions appreciated?
input {
xray_data {
file_name = ../testmtz.mtz
labels = "I(+),SIGI(+),I(-),SIGI(-)"
r_free_flags {
file_name = ../SePeak.hkl
label = TEST
test_flag_value = 1 }}
Sorry: R-free flags not compatible with F-obs array: missing flag for 2
F-obs selected for refinement.
This appears to arise from the SePeak.hkl having
Number of Miller indices: 9198
but the testmtz.mtz having
Number of Miller indices: 9199 (where is the extra reflection coming
from?)
by converting the SePeak.hkl to an mtz and dumping, I get SePeak.hkl.mtz
and testmtz.mtz
label #valid %valid min max type
H 9198 100.00% 0.00 14.00 H: index h,k,l
K 9198 100.00% 0.00 10.00 H: index h,k,l
L 9198 100.00% 0.00 135.00 H: index h,k,l
hkl 9198 100.00% 0.00 1.00 I: integer
H 9199 100.00% 0.00 14.00 H: index h,k,l
K 9199 100.00% 0.00 10.00 H: index h,k,l
L 9199 100.00% 0.00 135.00 H: index h,k,l
I(+) 9199 100.00% -39.40 32280.10 K: I(+) or I(-)
SIGI(+) 9199 100.00% -1.00 771.20 M: standard deviation
I(-) 6529 70.98% -32.00 16383.20 K: I(+) or I(-)
SIGI(-) 6529 70.98% 5.20 293.30 M: standard deviation
Thanks Mark
> Dear Mark,
>
> I believe your could simply define explicitly the columns in your
> input .def file for phenix.refine, I have done so previously with
> great succes.
>
> I guess the keywords you are looking for is:
> xray_data.file_name
> xray_data.labels
> xray_data.r_free_flags.file_name
> xray_data.r_free_flags.label
>
> And phenix.refine should put it in a nice .mtz file for you :-)
>
> Hope this helps.
>
> Regards,
> Folmer
>
>
>
>
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
>
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