[phenixbb] Appropriate model_vs_data usage over part of a structure

Andy Watkins andy.watkins2 at gmail.com
Wed May 25 09:31:00 PDT 2016

Perhaps necessary preface: I am largely learning as I go, and large parts
of Phenix (and the details of refinement data file formats) are still black
boxes for me.

Suppose I have a model of one chain of a complex and an .mtz describing the
entire complex. I have performed some refinement procedure altering the
model of that single chain.

My aim is to determine how this refinement procedure has affected the fit
to the experimental data--or, really, the subset of the experimental data
expected to be relevant for my model.

For obvious reasons,

phenix.model_vs_data chain_A.pdb whole_complex.mtz
phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz

are undesirable: they evaluate the model of a single chain against the
whole complex's data, and there's obviously a lot of unsatisfied electron
density. So, while this command *works*, it reports an unrepresentative
fit. (In theory, one solution to my problem would be to re-combine each
chain's refined version, then run model_vs_data on the recombined, refined
complex. I'm interested nonetheless in how it would work on the chains

Now, during the refinement procedure, we of course generate .ccp4 density
maps for the individual chain models:

phenix.maps chain_A.pdb whole_complex.mtz

which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz.
Attempting to employ that resulting .mtz file, i.e.

phenix.model_vs_data chain_A.pdb whole_complex.mtz
phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz

leads to an evocative error: Sorry_No_array_of_the_required_type: No
reflection arrays available.

My highest suspicion is that I need to alter maps.params in a particular
way so that reflection arrays are also output to model_map_coeffs.mtz. I
could also imagine that I need to be using another program entirely!

Thanks in advance for whatever help you can provide; unfortunately, I can't
provide any input files.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160525/4dfd29d5/attachment.htm>

More information about the phenixbb mailing list