On Thu, 2011-12-08 at 17:49 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
> I tried to look at all density regions bit by bit, but the density for
> the protein atoms always interfere with my vision. Is it possible to
> mask out
> the density of protein atoms,
Isn't that what difference density map is for?
Usually one simply generates the ligand model by using prodrg and/or
sketcher (which would give you a monomer description) and then tries to
manually dock it into the density in coot. Some automation is available
(e.g. coot can search for a ligand in the difference map throughout the
cell), but I believe it does not substitute for the manual inspection
(and, imho, neither is such complete replacement possible or even
desirable).
Things appear to be tricky in your case - at 1.25A a well ordered ligand
should produce clearly interpretable density. What you are describing
sounds like either disordered ligand or indeed solvent molecules, or the
mix of the two (the worst-case scenario). Ultimately, it is up to you
to interpret the density, but be careful to curb your imagination.
You may be able to get a better advice if you post the density
snapshots.
Cheers,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
