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
