Dear James, Thankyou for this interesting summary analysis. Just at the end of your message I would remark about "nomenclature". I meant to reply before in a recent thread about resolution terminology issues but was focussed on CCP4.
So, just to say that as a community we have three categories of approach on such:- Terminology in reasonably common use but with significant variations; not much we can do about this variance but it is valuable to air such on this bulletin board. Dictionary terms we might offer the IUCr wiki project; ie where terms are widely agreed upon. Nomenclature issues of merit to be formally resolved by the IUCr Nomenclature Committee; proposals can be put to the Chairman (Prof Authier). One fairly recent deliberation ruled in favour of brightness over brilliance for SR source emissions. Another case was a ruling in favourite of standard uncertainty versus esd. Another was ADP versus Thermal parameter. Etc. Greetings, John Prof John R Helliwell DSc On 17 Jan 2011, at 17:46, James Holton <jmhol...@lbl.gov> wrote: > On 1/15/2011 12:28 PM, REX PALMER wrote: >> >> Does anyone know of a statistical breakdown of successful protein structure >> determinations in terms of the method used? >> >> Rex Palmer >> Birkbeck College > > I think this was discussed back in April under "Proportion of MR in PDB": > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;b5186393.1004 > > I did a little analysis then where I manually distilled the 860 unique > strings found under the "METHOD USED" entry of the PDB down into what I think > are distinct "methods": > 37851 MR > 16435 "NULL", "N/A", or no "REMARK 200" record at all > 7802 MAD/SAD > 993 MIR > 669 OTHER > 352 SIRAS > 316 MIRAS > 188 AB-INITIO > 88 SIR > 6 RIP > 2 UNCONVENTIONAL > 1 UNCONVENTIANAL > 1 N? > 1 FIBER-DIFFRACTION > 64776 total > > Note, that the second most popular "method" seems to be no method at all, so > I suppose that puts some large "error bars" on these numbers. > > Although it is somewhat disturbing that such a large number of people didn't > seem to think their "method" was worth mentioning in their PDB deposit, I > don't this is because "methods" in general are considered unimportant. It is > because the "method" is considered obvious. There are a lot of > crystallographers out there who only know one "method". I am often amused > when I witness a meeting of two crystallographers who are each shocked to > learn that the other not only doesn't use their favorite computer program, > but has also never heard of it! > > I am willing to bet that the earliest "no method" entries (particularly the > ones that lack a REMark 200 record) were probably MIR, since that was the > "obvious" method to solve a structure for some time. Modern "NULL" entries > seem to be mostly what I call "molecular replacement", which includes just > refining from a native, etc. not necessarily running an MR search program. > Or, at least, there are only ~26700 entries that explicitly state that the > "method used to determine the structure" was "molecular replacement", the > rest I assigned to this "bin" because the entry mentions a "starting model", > etc. > > In general, there is definitely confusion about nomenclature! For example > some structures that claim to be "Ab-initio" are actually MAD/SAD structures. > Although historically I think "Ab-initio" is supposed to be synonymous with > direct-methods based structure determinations. > > -James Holton > MAD Scientist >
