Thanks to everyone who responded. I appreciate your pointing out the caveats of such statistics mining expeditions.
I remember (with no accuracy or precision) sitting in a lecture by Wayne Hendrickson years ago and watching him cringe at the notion of considering the simple case of difference Fourier (say, isomorphous protein and protein+ligand structures) as Molecular Replacement. Like you point out, Thierry, I believe he referred to these cases as Molecular Substitutions. And like you said, there's no consensus with the nomenclature. Phil, thanks much for the stats. Somewhat reassuring that they are somewhat similar to what I got from the PDB. Thanks to everyone! Raji On Mon, Apr 15, 2013 at 11:46 AM, Phil Jeffrey <pjeff...@princeton.edu>wrote: > From my own db program: > > Number of entries in histogram: 711 > Total number of instances : 78467 > 0 48249 0.6149 MOLECULAR REPLACEMENT > 1 8557 0.1091 NULL > 2 5632 0.0718 SAD > 3 5128 0.0654 MAD > 4 3600 0.0459 FOURIER SYNTHESIS > 5 1762 0.0225 OTHER > 6 1171 0.0149 MIR > 7 511 0.0065 SIRAS > 8 505 0.0064 DIFFERENCE FOURIER > 9 392 0.0050 MIRAS > 10 229 0.0029 AB INITIO > 11 226 0.0029 MR > 12 151 0.0019 RIGID BODY REFINEMENT > 13 146 0.0019 ISOMORPHOUS REPLACEMENT > 14 110 0.0014 AB INITIO PHASING > 15 109 0.0014 MULTIPLE ISOMORPHOUS > 16 83 0.0011 N/A > 17 75 0.0010 SIR > 18 70 0.0009 RIGID BODY > 19 64 0.0008 DIRECT METHODS > 20 50 0.0006 RE-REFINEMENT USING > 21 37 0.0005 DIFFERENCE FOURIER PLUS > 22 36 0.0005 ISOMORPHOUS > 23 34 0.0004 REFINEMENT > 24 30 0.0004 MOLREP > 25 26 0.0003 SE-MET MAD PHASING > 26 25 0.0003 RIGID-BODY REFINEMENT > 27 24 0.0003 ISOMORPHOUS METHOD > etc > > It's a very heterogeneous field, that REMARK 3 field, and the ones above > are the most dominant entries (note the 8,557 that are "NULL" that are in > fact crystal structures). At least in some versions of ADIT the guidance > that RCSB gives about this field is very weak, which accounts for the > variation. > > I'm interested in what "ab initio phasing" really means, but I've been too > lazy to mine the actual entries for details. > > Phil Jeffrey > Princeton > > > > On 4/15/13 9:48 AM, Raji Edayathumangalam wrote: > >> Hi Folks, >> >> Does anyone know of an accurate way to mine the PDB for what percent of >> total X-ray structures deposited as on date were done using molecular >> replacement? I got hold of a pie chart for the same from my Google >> search for 2006 but I'd like to get hold of the most current statistics, >> if possible. The PDB has all kinds of statistics but not one with >> numbers or precent of X-ray structures deposited sorted by various >> phasing types or X-ray structure determination methods. >> >> For example, an "Advanced Search" on the PDB site pulls up the following: >> >> Total current structures by X-ray: 78960 >> 48666 by MR >> >> 5139 by MAD >> >> 5672 by SAD >> >> 1172 by MIR >> >> 94 by MIR (when the word is completely spelled out) >> >> 75 by SIR >> 5 by SIR (when the word is completely spelled out) >> >> That leaves about 19,000 X-ray structures either solved by other phasing >> methods (seems unlikely) or somehow unaccounted for in the way I am >> searching. Maybe the way I am doing the searches is no good. Does >> someone have a better way to do this? >> >> Thanks much. >> Raji >> >> -- >> Raji Edayathumangalam >> Instructor in Neurology, Harvard Medical School >> Research Associate, Brigham and Women's Hospital >> Visiting Research Scholar, Brandeis University >> >> > -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
