[phenixbb] Appropriate model_vs_data usage over part of a structure

Christian Roth christianroth034 at gmail.com
Wed May 25 10:28:36 PDT 2016

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


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 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/df6ec8b8/attachment.htm>

More information about the phenixbb mailing list