Dear Remy and Faisal -
Just a geeky bioinformatics note: searching my local copy of the PDB
(somewhat out of date), shows that 22,165 out of 72,000 structures
contain a 'REMARK 470' line, which is how the PDB notes that atoms are
missing from a residue. Some of these are no doubt mistakes by the
depositors, but most probably reflect the decision to remove invisible
side chain atoms from the coordinates (e.g. trimming back to Cbeta)
while keeping the correct residue name.
I think we can all agree that virtually every structure in the PDB will
have a few residues where some of the atoms are not visible in the
density. So the "trim the side chains" crowd is a well-represented
minority at 30%, but 70% of depositors chose another option.
I personally like to leave all atoms on the side chains; they look wrong
to me when beheaded. I just try to put the invisible atoms in a
stereochemically plausible conformation, leave the occupancy set to 1,
and let the refinement program deal with them.
- Matt
On 11/9/12 3:47 PM, Remy Loris wrote:
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
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
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