[phenixbb] Reflection file woes phenix/ccp4/PDB

[Pavel Afonine]

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!
>
> MM
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