Dear Eric Bennett, 3g6a was processed by PDB_REDO (without the original R-free set which sadly wasn't deposited) on Monday, 20 July 2009 at 21:35 CEST with PDB_REDO version 2.6: http://www.cmbi.ru.nl/pdb_redo/g6/3g6a/index.html That was roughly two months after the last revision (the entry is replaced each time the timestamp of either the PDB or SF file changes). Okay, it is not done instantly but we keep up with the PDB reasonably well. If you cannot find the PDB_REDO entry directly, you can always try the link on the PDBe entry page.
You are quite right saying that EDS and PDB_REDO do not work for all structures. They do however work for 98% of all structures (at least PDB_REDO does). Of the 2% percent that is missing, 1% is caused by things we understand and are annotated in WHY_NOT (www.cmbi.ru.nl/WHY_NOT), the other 1% is caused by cases where we cannot reproduce R(-free) to within 10 percentage points. We are currently investigating those and the PDB has been a great help in that. Oh, and PDB_REDO does take twinning into account (at least to the extent Refmac does). You were also right about the list of all entries. We recently moved to a newer version of WHY_NOT which broke the link. My bad, I have fixed it. On topic: I think the deposition of maps is a waste of space. Maps may describe what the depositors <paranoid>want you to think they</paranoid> have looked at. But that does not mean they looked at the right thing. Who knows what they did to the maps in terms of (unwarrented) density modefication to make them look cleaner? The advantage of the EDS is that it is impartial and uniform. The maps are generated in a clear and well-described way. Cheers, Robbie ---------------------------------------- > Date: Sat, 12 Dec 2009 10:33:04 -0500 > From: er...@pobox.com > Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....=?UNKNOWN?Q?=FE?= > To: CCP4BB@JISCMAIL.AC.UK > > >Dear Fred, > > > >People have already done this for all PDB entries: > >- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats > >- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the > >stats and maps do improve most of the time, unfortunately also for > >structures that are not "old" (but to a lesser extent). > > Except it doesn't work for _all_ PDB entries, even when SF are > available. On your site, for example, the "Current entries" link on > the home page seems to be broken and entry 3G6A (which was released 8 > months ago) is not available for some unspecified reason. > > For some cases (like twinned structures) EDS won't have a map. > > Rather than relying on availability of a third party server to enable > viewing the map, it would be a much cleaner solution if authors just > deposited their own maps in the PDB. > > --
