[phenixbb] help with validating a very low res structure

Francis E Reyes Francis.Reyes at colorado.edu
Thu Apr 5 18:37:01 PDT 2012


And I thought I had it tough interpreting 5A maps from experimental phases. I didn't think that anyone would be working at worse (ok except maybe Nenad Ban or Kiyoshi Nagai). And with molecular replacement even!

What exactly are you trying to validate at this low resolution? That your MR solution isn't biased?  

 On Apr 5, 2012, at 6:55 PM, Yunji Wu wrote:

> Hi there-- 
> Any old school experimental phasing experts want to help me out? 
> I have an 8 angstrom structure solved using molecular replacement, refined to Rwork 0.38 and Rfree of 0.47. I also have a heavy atom (not SeMet) derivative data set to 10 angstroms. The idea is to get as much information from these data as possible so as to validate my current MR model. My approach is to calculate a difference map using the isomorphous difference Fouriers OR anomalous difference Fouriers as the amplitudes, with phases derived from the MR model-- then using the difference map to locate putative heavy atom sites. I would use various controls and experiments to (computationally) validate the credibility of these sites (e.g. cross-phasing with only iso/ano differences). Anyone have any suggestions for how to do this using Phenix? I use the GUI (generally the nightly builds), and am a newcomer to Phenix.  
> Thanks!!
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