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Re: [ccp4bb] generating omit maps |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: generating omit maps From: Mischa Machius Mischa {- dot -} Machius {- at -} UTSOUTHWESTERN {- dot -} EDU Date: 2008-12-11 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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