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Hi, There has been quite a lot of discussion about this and I think different opinions exist. I would try to keep the side chains, if there is some evidence where they are. Otherwise I would just delete atoms and I would not mutate them to alanine. http:[log in to unmask] Best regards, Lari ______________________________________________________ Lari Lehtiö, PhD, Adjunct Professor Biocenter Oulu Department of Biochemistry P.O.Box 3000 FIN-90014 University of Oulu Finland http://cc.oulu.fi/~llehtio/ _____________________________________________________ Quoting Faisal Tarique <[log in to unmask]>: > 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..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 >