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On Friday, 09 November 2012, Faisal Tarique wrote: > Dear all > > i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22 > and 25 respectively..the Ramachandran plot shows 90% of the residues in the > most favorable region and with 6 residues in generously allowed and no > residues in disallowed region. But in some areas i can see density missing > for side chains ( in loop regions )..i have question do i need to mutate > them to alanine or leave them as such. Mutating to alanine is not an option. They are not alanine. If nothing else, when you get to the point of depositing your structure in the PDB it will fail validation checks because the sequence is not correct at those points. But if you mean should you delete sidechain atoms beyond CB, that is another question. That is a legitimate option. I suggest trying that and then looking in difference density maps to see if any density shows up to guide placement of the sidechain. Ethan > .The density fit analysis in COOT ( > traffic light) showing those regions with side chain as red.. > > thanx in advance > > Regards > > Faisal > School of Life Sciences > JNU >