[phenixbb] differentiate Glu/Gln and Asp/Asn from Electron Density?

Pavel Afonine pafonine at lbl.gov
Wed Feb 10 22:48:51 PST 2016

Hi Kaushik,

I think that's what Phenix Autobuild does: it ranks possible residue 
fits into map-candidate by probability taking into account density 
shapes, sequence and may be other factors.
See around pages 62-64 here:



On 2/10/16 22:14, Kaushik Hatti wrote:
> Hello,
> In continuation to my earlier thread (subject: sequence independent 
> model building possible?), I have built model into density without 
> knowledge of sequence for a data diffracted to 1.9A resolution.  
> Current R/Rfree is 15/19, phaser error=16.88 degrees with no 
> Ramachandran outliers.
> Is there a way we can differentiate between Glu/Gln, Asp/Asn and 
> sometimes Thr/Val directly from density?  I have considered the local 
> environment (hydrophobic/hydrophilic/polarity pockets, possible 
> hydrogen bonds/other interactions, buried/exposed, etc...) in choosing 
> one over the other confusing pairs of amino acids.  However, I am not 
> absolutely certain in many places.
> A BLAST of this sequence against all non-redundant protein sequence 
> database yield highest hit of 80% sequence identity. Hence, we are 
> still not sure of sequence of the contaminant protein which got 
> crystallised and want to decipher sequence directly from the structure.
> Thanks for any pointers/suggestions,
> Regards,
> Kaushik
> -- 
> Stupidity is everyone’s birthright.  However, only the learned 
> exercise it!
> --Kaushik (28Oct2014)
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