[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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