Let me also follow up on this point. I also agree that the ligand should be added very late in the refinement/model-building procedure. I also encourage people in my group to create a subdirectory "BEFORE_LIGANDS" into which they put the current PDB and map (or mtz) files prior to adding the ligand. Putting it into a separate directory avoids accidentally deleting it if you tidy up your modeling files at some later state.
Come publication time, include in your manuscript the map generated at this stage prior to inclusion of the ligand. It is sometimes not as pretty but it gives the reader a honest view of your ligand density. Cheers, Andy -- Andrew M. Gulick, Ph.D. ----------------------------------- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 ----------------------------------- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 12/10/08 10:41 AM, "Mischa Machius" <[EMAIL PROTECTED]> 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
