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
