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
