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...
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
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
