[phenixbb] reflection files, anomalous data, and test set

[Folmer Fredslund]

2008/7/23 Mark Collins <mcollins at convex.hhmi.columbia.edu>:
> Hi
> I have been using a SePeak.hkl file in my refinement (CNS, and then
> switched to Phenix).
>
> This was created from SePeak.sca to SePeak.mtz and then to SePeak.hkl with
> ccp4i's (scalepack2mtz and mtz2various).  I want to try using the group
> anomalous command to see is my Rfree decrease with the inclusion of the
> anomolous data.
>
> The problem I am encountering is that the SePeak.hkl contains no
> anomolous inforomation.  If I make a new mtz (I have used
> reflection_file_converter to create a new SePeak#2.mtz from my original
> SePeak.sca and this does contain + and - columns) I can't find a way
> to merge the test set from the SePeak.hkl file.  And generating a new test
> set raises othere issue that have been discussed in this bb before.
>
> Does this make sense?  And is there a way to merge a test set from one
> file and a F or I obs.
>
> Mark
> _______________________________________________


Dear Mark,

I believe your could simply define explicitly the columns in your
input .def file for phenix.refine, I have done so previously with
great succes.

I guess the keywords you are looking for is:
xray_data.file_name
xray_data.labels
xray_data.r_free_flags.file_name
xray_data.r_free_flags.label

And phenix.refine should put it in a nice .mtz file for you :-)

Hope this helps.

Regards,
Folmer




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