On Dec 10, 2008, at 9:52 AM, Mark J. van Raaij wrote:
as a small variation on this, I would first "finish" the protein,
and then include ligands, working from larger to smaller (ATP =>
citrate => glycerol => sulphates => waters). Sometimes several
waters (from automated solvent building) in place of a bona fide
ligand (or a glycerol for example) refine eerily well and give
reasonable maps...
Automated solvent building that includes automatic refinement should
probably be banned ;)
I usually add solvent molecules before adding ligands. For one, the
electron density usually improves when adding solvent, so that the
interpretation of the ligands becomes easier. I would recommend to
check every single solvent molecule, i.e., never use automatic solvent-
modeling and refinement (!) routines blindly. Make sure to remove
those solvent molecules that have clearly been placed into ligand
density before doing the actual refinement.
Another potential problem may have to be taken into consideration as
well: depending on the resolution, it can happen that protein side
chains are being moved into ligand density if it is not occupied by
some atoms. In such cases, I use a mixed strategy derived from the
approaches described in my first post.
Best - MM
On 10 Dec 2008, at 16:41, Mischa Machius wrote:
Kathleen - The easiest way is to simply remove the ligand from the
coordinates and refine for a few cycles. Whether that is
particularly meaningful is another question. Better would be to
remove the ligand coordinates, "shake" the remaining coordinates
(i.e., randomly displace them by a small amount), and then refine.
Even better, perhaps, would be to calculate a simulated-annealing
omit map, but AFAIK, you can't use CCP4 for that. IMHO, the best
option is to not include the ligand in the model-building and
refinement processes until all of the protein(s), solvent
molecules, etc. have been properly modeled. I personally tend to
include ligands only at the very end of the modeling/refinement
process, unless there is really no ambiguity. This strategy will
minimize any model bias from the ligand, and it will give you an
omit map by default (until you actually include the ligand). Best -
MM
--------------------------------------------------------------------------------
Mischa Machius, PhD
Associate Professor
Department of Biochemistry
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
On Dec 10, 2008, at 9:30 AM, Kathleen Frey wrote:
Hi Everyone,
Can anyone tell me a relatively easy way to generate an omit
density map for a ligand? I know that CNS can do this, but I was
wondering if there's a CCP4 related program to generate omit maps.
Thanks,
Kathleen
