Here are my "counts" of the various methods used for PDBs as of a few
days ago:
37851 MR
7802 MAD/SAD
7777 NULL
669 OTHER
53 N/A
993 MIR
352 SIRAS
316 MIRAS
188 AB-INITIO
88 SIR
6 RIP
2 UNCONVENTIONAL
1 UNCONVENTIANAL
1 FIBER-DIFFRACTION
56171 TOTAL
The other 8605 don't have REM200 entries.
Note that creating this list involves some heuristics on my part. For
example PDB files that don't say how they were solved, but mention
another PDB entry as the source of "phases" are put into the "MR" bin.
I should also note that the 5:1 ratio of MR:MAD/SAD is consistent with
the 5:1 ratio of "native" to "anomalous" datasets I see collected at my
beamline (Advanced Light Source 8.3.1). This is despite the fact that
an average of 10 MAD/SAD datasets are collected for every one that gets
solved.
-James Holton
MAD Scientist
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
