Hi Mischa, thanks for sending the data file. 1) The file passes this simple sanity check: python run.py where run.py contains the code inclosed between "******": ****** from iotbx import reflection_file_reader def run(): reflection_file = reflection_file_reader.any_reflection_file( file_name="data.mtz") miller_arrays = reflection_file.as_miller_arrays() cntr = 0 for ma1 in miller_arrays: if(ma1.info().labels[0].count("free")): assert ma1.data().count(1)+ma1.data().count(0) == ma1.data().size() assert ma1.data().count(1) < ma1.data().count(0) cntr+=1 for ma2 in miller_arrays: assert ma1.indices().all_eq(ma2.indices()) assert cntr == 1 if (__name__ == "__main__"): run() ****** - I don't see any anomalies in the output of phenix.mtz.dump data.mtz command: Processing: data.mtz Title: /Users/machius/Work/_Projects/Kuhlman/bd2/03-ReflectionFiles/bd2-h35e- Space group symbol from file: P212121 Space group number from file: 19 Space group from matrices: P 21 21 21 (No. 19) Point group symbol from file: 222 Number of crystals: 2 Number of Miller indices: 38549 Resolution range: 26.345 1.15068 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (37.241, 46.528, 62.277, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal Project: project Id: 2 Unit cell: (37.241, 46.528, 62.277, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 1 Number of columns: 9 label #valid %valid min max type H 38549 100.00% 0.00 32.00 H: index h,k,l K 38549 100.00% 0.00 40.00 H: index h,k,l L 38549 100.00% 0.00 54.00 H: index h,k,l I-obs(+) 38249 99.22% -120.50 106929.00 K: I(+) or I(-) SIGI-obs(+) 38249 99.22% 1.00 3348.00 M: standard deviation I-obs(-) 34269 88.90% -221.00 100983.00 K: I(+) or I(-) SIGI-obs(-) 34269 88.90% 1.90 3140.00 M: standard deviation R-free-flags(+) 38249 99.22% 0.00 1.00 I: integer R-free-flags(-) 34269 88.90% 0.00 1.00 I: integer So I would say everything is ok with your data file and you should probably talk to PDB people to resolve the issue they have with your file. Pavel On 12/15/11 8:40 AM, Machius, Mischa Christian wrote:
Y'all,
While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing.
The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928.
Indeed, using this file in CCP4 fails with the message: "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q"
The file contains anomalous data. I have no problems with files that do not contain anomalous data.
Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility.
When I use iotbx.reflection_file_reader, I cannot detect any anomalies.
I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them.
Anybody ran into this issue before? Any ideas for how to resolve it?
Many thanks in advance!
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