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
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