Dear Faisal,
You definitely do not mutate to alanine as that would imply for the
future "user" of your pdb file that it is a mutant.
Some people feel they have to keep the side chain but put the
occupancies at zero. I think this is a bad practice and strongly oppose
to it as for the future "user" of your deposited pdb file, who often is
not a crystallographer, you suggest a specific conformation for your
side chain that may be interpreted in terms of biology, while in reality
it addopts a huge, disordered ensemble of conformations.
Personally I am of the opinion that you should simply remove the side
chain atoms (but keep the residue name). And that is the same as what
you do with a whole loop that is disordered. I think it is lso the most
common practice in deposited structures.
Remy Loris
Vrije Universiteit Brussel
On 09/11/12 20:22, 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..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
