[phenixbb] Appropriate model_vs_data usage over part of a structure

Pavel Afonine pafonine at lbl.gov
Wed May 25 17:16:51 PDT 2016

Hi Andy,

> Suppose I have a model of one chain of a complex and an .mtz 
> describing the entire complex.

I'm struggling making sense of this statement.. MTZ file is just a file 
format to records some data with labels associated with it in a binary 
form to make it easier for machines to handle it. So what precisely you 
mean by ".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.

Okay. This is what refinement is for.

> 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.

Could you please define "unrepresentative fit" in this context?

> (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.

I guess Fobs would not like this as they include contributions from all 
atoms, as far as I remember from the theory..

> 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

Well, this is what it seems *you* do as part of *your* protocol, but 
this is *not* what typical work-flow includes as phenix.refine always 
reports maps upon completion of refinement; so running phenix.maps seems 
to be an unnecessary step in this scenario.

> 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.
Hm.. I afraid I'm lost now: model vs data tool is not supposed to accept 
inputs other than original data, Iobs or Fobs, and model files.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160526/ca422d75/attachment.htm>

More information about the phenixbb mailing list