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://www.mail-archive.com/[email protected]/msg20437.html
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 <[email protected]>:
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
