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: http://phenix-online.org/presentations/model_building_resolve_tt_2011-02-09.... Pavel 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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