[phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

Dale Tronrud det102 at uoxray.uoregon.edu
Wed Jan 2 16:36:27 PST 2008


    Requested mtz.dump inserted later in letter.

Pavel Afonine wrote:
> Hi Dale,
> 
>>> 1) Why you specify reflection MTZ file twice in phenix.refine script?
>>>
>>>     
>>     I put the mtz in twice because if I put it in once phenix.refine
>> complains that I have no free R flags.  It seems to want one file with
>> the amplitudes and another with the flags.  Since I have both in the
>> same file I put that file on the line twice and phenix.refine finds
>> everything it needs.
>>   
> 
> phenix.refine looks for free-R flags in your main data file 
> (1M50-2.mtz). Optionally you can provide a separate file containing 
> free-R flags (I have to write about this in the manual). However, if 
> your  1M50-2.mtz contains free-R flags then you don't need to give it 
> twice. So clearly something is wrong at this step and we need to find 
> out what is wrong before doing anything else. Could you send the result 
> of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your 
> data file? Or I can debug it myself if you send me the data and model.
> 

dale at fluorine [2] phenix.mtz.dump 1M50-2.mtz
Processing: 1M50-2.mtz
Title: [No title given]
Space group symbol from file: P 43 3 2
Space group number from file: 212
Space group from matrices: P 43 3 2 (No. 212)
Point group symbol from file: PG432
Number of crystals: 2
Number of Miller indices: 45448
Resolution range: 119.572 2.14861
History:
   From FREERFLAG  8/12/2007 00:31:08 with fraction 0.050
   From f2mtz  8/12/2007 00:31:02
   data from CAD on  8/12/07
Crystal 1:
   Name: HKL_base
   Project: HKL_base
   Id: 1
   Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
   Number of datasets: 1
   Dataset 1:
     Name: HKL_base
     Id: 0
     Wavelength: 0
     Number of columns: 4
     label      #valid  %valid  min   max type
     H           45448 100.00% 0.00 45.00 H: index h,k,l
     K           45448 100.00% 1.00 78.00 H: index h,k,l
     L           45448 100.00% 0.00 55.00 H: index h,k,l
     FreeR_flag  45448 100.00% 0.00 19.00 I: integer
Crystal 2:
   Name: allen-2002
   Project: FMO-ct
   Id: 2
   Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
   Number of datasets: 1
   Dataset 1:
     Name: 1
     Id: 1
     Wavelength: 0
     Number of columns: 2
     label #valid %valid  min      max type
     FP     41607 91.55% 0.00 15171.00 F: amplitude
     SIGFP  41607 91.55% 0.00  1716.00 Q: standard deviation

>>     If the MD5 hash of the test set depends on the resolution then certainly
>> I could be in trouble.  
> 
> No. It must always use the original files before any processing.
> 
>>     Does the resolution limit affect the MD5 hash of the test set?
>>   
> 
> No.  If it does then it is a very bad bug. I will play with this myself 
> later tonight.
> 
>>   
>>> 3) Does this work:
>>>
>>> (...)
>>     I'll try these but it will take a bit of time.
>>   
> 
> Don't run it until completion. Just make sure it passed through the 
> processing step.
> 
> Pavel.
> 
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