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On 26 Jun 2006, at 23:02, Jacob Corn wrote:
I think coot might be asking for the name as defined in the monomer
library.
Yes.
You can find that in
<coot directory>/share/coot/lib/data/monomers/mon_lib.list
<coot directory>/share/coot/lib/data/monomers/mon_lib.html
These are basically identical to refmac's mon_lib.
The monomer library distributed with Coot *is* the Refmac library.
There are a LOT of monomers in there, so paging through every monomer
one at a time will take forever. Instead, as you say, I would use your
knowledge of things like crystallization condition, protein cofactors,
etc. to make a shorter list of candidates and then examine those
carefully.
Sketcher can search the monomer library. Coot will do so soon too.
Debanu Das wrote:
> What I would like to do is to read in some kind of library with
ligands and then try to fit them into the density
> one at a time to see how they fit and to try to deduce what the
ligand may be. I was hoping to do this by
> reading in the COOT library and trying out the ligands one by one.
Coot will attempt to fit every ligand that you provide into every
"blob" - it provides the best fit for each "blob".
You will have to provide a molecule/coordinates for each potential
ligand (you can do this using libcheck, as you
have discovered).
Paul.
