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Re: [ccp4bb] Proportion of MR in PDB |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Proportion of MR in PDB From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK Date: 2010-04-19 Jim Pflugrath calls it "molecular substitution" -- I find this a very neat distinction. On 19/04/2010 15:50, Ian Tickle wrote: > I would say it should still be classed as MR: the distinguishing > feature of MR is surely that it uses an known structure as a starting > model, not that it does a rotation/translation search. In any case > the distinction between a rigid-body search and RB refinement is moot. > At Astex our automated scripts routinely do a limited MR search for > all our protein-ligand structures, even though it may not be necessary > in all cases. This is because we have found from experience that RB > refinement alone is often not sufficient: presumably the degree of > non-isomorphism induced by soaking and/or freezing the crystals (e.g. > we often see 5-10% changes in cell parameters) takes it beyond the > radius of convergence of the refinement. We use a limited search MR > to avoid issues of finding symmetry-related or origin-shifted > solutions. > > Cheers > > -- Ian > > On Mon, Apr 19, 2010 at 3:06 PM, Edward A. Berry > >> Quite a lot of structures in the PDB involve minor variations on structures >> that have already been solved (different ligands, mutants, high res), so the >> "solution" involves refining the previous structure against the new data, >> perhaps starting with rigid body refinement to correct minor variations >> in cell parameters. >> Would you include this in "molecular replacement"? >> >> Ed >> >> Nicholas Keep wrote: >> >>> Thanks to several people for helpful comments to my question on the >>> Proportion of MR in the PDB. >>> >>> I got two very detailed responses one from the OCA team at the Weizmann >>> which went to the Bulletin Board >>> >>> "This is what OCA has: From un total of 64,623 PDB structure files, >>> 30,784 have 'MOLECULAR REPLACEMENT' as Method for Structure Determination. >>> >>> However, you must remember that we have a large number of false negatives >>> Several reasons: >>> >>> - Only 47,557 structure files from the total of 64,623 report which >>> method was used for structure determination. For example, 1CRY whose >>> title reports using the MR method does not include the info in the >>> proper REMARK. >>> >>> - Users are allowed to write almost anything as the METHOD USED TO >>> DETERMINE >>> THE STRUCTURE, making it difficult an accurate report. OCA found PDB >>> italian >>> speaking structure files reporting 'MOLECULARE REPLACEMENT' ... >>> This and other problems are being reported to RCSB." >>> >>> >>> >>> and one from U of Virginia >>> >>> "Based on information from Remark200 lines, 31761 structures were solved >>> using MR, what comprise for 56.8% of all X-RAY structures (55843). >>> Considering structures which were determined using 'primitive MR' the >>> number grows to 34949 (62.6%). There are also some structures determined >>> using combination of MR with SAD, MAD, SIR and MIR. If we would add them, >>> the number will increase to 35258 (63.1%)." >>> >>> Thanks again >>> Nick >>> >>> >>> >> CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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