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 <ber...@upstate.edu> wrote: > 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 >> >> >
