[phenixbb] differentiate Glu/Gln and Asp/Asn from Electron Density?
pafonine at lbl.gov
Wed Feb 10 22:48:51 PST 2016
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:
> 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,
> Stupidity is everyone’s birthright. However, only the learned
> exercise it!
> --Kaushik (28Oct2014)
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