[phenixbb] Appropriate model_vs_data usage over part of a structure

Andy Watkins andy.watkins2 at gmail.com
Wed May 25 10:38:59 PDT 2016


Thanks--that certainly makes sense. In that case, I suppose I have a
different question: what distinguishes the .mtz file suffixed "map_coeffs,"
which is output by phenix.maps, from the input .mtz?

On Wed, May 25, 2016 at 1:28 PM, Christian Roth <christianroth034 at gmail.com>
wrote:

> You might look for the Real space correlation coefficient to see if your
> model fit that particular map better than before, but thats probably it.
>
> There is no subset experimental data just influenced by one chain. The
> whole complex contributes to each measurement and vice versa your chain A
> model contribute to each measurement you made to generate the maps. Sorry,
> but that's it
>
> Christian
> Am 25.05.2016 um 17:31 schrieb Andy Watkins:
>
> 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
> separately.
>
> 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.
>
>
> _______________________________________________
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160525/453e6c8d/attachment.htm>


More information about the phenixbb mailing list