before modelling a long side-chain in non-existing or dubious density,
also make sure it is really there in the protein by sequencing your
expression plasmid. Your arginine (for example) may in fact be a
serine or glycine...databases are not 100% accurate and neither is PCR
if it was used in the cloning.
Quoting Ed Pozharski:
OK, here we go again.
This has been argued ad nauseam, see for example
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
or
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html
(hard to believe we have gone more than a year without another
version of "what to do with disordered side chains" 250-post long
discussion :)
I do not have much to add to the above, however
On 11/09/2012 05:22 PM, Matthew Franklin wrote:
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.
This maybe the historical average, I suspect that currently the
"trim the side chains crowd" may be at least at 50% (but what about
Ohio? :). Majority, however, is not always right (don't get me
started on I-over-sigma ratios).
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.
With all due respect, to model something where there is no density
(aka experimental evidence) cannot be justified by aesthetics. On
the contrary, there is some evidence suggesting that modelling
disordered side chains in the way you describe adds small, but
detectable error to the rest of the model.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es
