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

Pavel Afonine pafonine at lbl.gov
Fri Dec 28 17:12:22 PST 2007

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.

>     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.


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