On Mon, May 11, 2009 at 05:22:25PM -0500, Pete Meyer wrote: > > P.S. I would also appreciate the specific query type for searching the > > PDB on the web for phasing method (MR, MAD, SAD, MIR, etc.). They seem > > to have everything under the sun searchable, but I cannot find this one. > > Last time I emailed the RCSB about this (a few years back), it wasn't > possible to search by phasing method. You can try using advanced search > -> keyword search -> advanced and doing a full text search, but this is > somewhat less than ideal. To be fair though, I suspect relatively few > people searching the PDB are concerned about the phasing method used.
Funny, I was looking at that just the other day. You basically need a local copy of the PDB and do some ugly grep/awk into the PDB files ... at least thats what I do (there might be better ways). Anyway, as of 28.04.2009 we have a total of 48969 entries with a line REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: which show (no guarantee!): Molecular replacement = 26436 Undefined (i.e. NULL, N/A etc) = 9349 MAD = 4125 SAD = 3028 Fourier methods = 2929 MIR = 1706 SIR = 512 Direct methods, ab initio = 327 Rigid-body refinement = 186 RIP = 3 UNKNOWN (everything else) = 504 This might add up to more than the total number of entries, since some have several methods listed. I tried to accomodate mis-spellings - lots of them available: MOLECULARE REPLACEMENT MOLECULAR REPLECEMENT MOLECULAR REPLCEMENT MOLECULAR REPLACEMET MOLECULAR REPL. MOLECULAR REPACEMENT MOLECULAR REEMPLACEMENT MOLECULAR PLACEMENT MOLECULAR EEPLACEMENT MOLECULAR PLACEMENT DIFFERENT FOURIER DIFFERECE FOURIER DFIFFERECE FOURIER etc. Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
