Yep, phenix.refine also always creates one reflection file that contains map coefficients. In fact, it contains all together: - original Iobs (or Fobs - whatever the user specified); - Fobs used in refinement; - Fmodel (the total model structure factor including all scales, bulk-solvent etc), so one can readily recompute the R-factor; - freeR flags; - and map coefficients (mFo-DFc, 2mFo-DFc and 2mFo-DFc with missing Fo filled in with DFc).
The question is whether the PDB retains this information? Pavel On Tue, Jan 10, 2012 at 8:39 AM, Oliver Smart <osm...@globalphasing.com>wrote: > Including the final map coefficients as part of the structure factor file > deposited and then archived by the PDB provides a means to directly > see the actual map as interpreted by the crystallographer. EDS is useful > in providing a "third party view" but the actual map is really better. > > We think map deposition is a good idea and are working on tools to make it > easy to do with BUSTER. There are already a few recent (REFMAC) depositions > with map coefficients in the pdb (for instance 3u57). Displaying the maps > is currently a bit difficult, see ccp4bb > message (Wed, 21 Dec 2011): > > https://www.jiscmail.ac.uk/**cgi-bin/webadmin?A2=ccp4bb;**325e1870.1112<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112> > > Cheers, > > Oliver > > | Dr Oliver Smart | > | Global Phasing Ltd., Cambridge UK | > | > http://www.globalphasing.com/**people/osmart/<http://www.globalphasing.com/people/osmart/>| > > On Tue, 10 Jan 2012, Robbie Joosten wrote: > > Hi Frank, >> >> EDS already does that. Even so, reproducing the R-factor does not prove >> that >> the map is reliable. See for instance 3frk for which the deposited dataset >> is much smaller and less complete than the one used for refinement. The >> map >> from EDS is therefore completely model biased. >> I only recently started looking for this problem of lower-than-reported >> completeness with. I have not found a lot of cases, but already too many. >> Fortunately, at least a few depositors deposited the rest of the dataset >> after I sent a bug report to the PDB (e.g. 3mbs). >> >> Cheers, >> Robbie >> >> -----Original Message----- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> Frank von Delft >>> Sent: Tuesday, January 10, 2012 16:23 >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] reliable/unreliable maps? >>> >>> Or just print both Rfactors...? >>> >>> >>> On 10/01/2012 15:21, Luca Pellegrini wrote: >>> >>>> Hi Paul, >>>> >>>> >>>> What would you rather it say, I'm happy to change the message. "The EDS >>>>> >>>> does not think that this is a reliable map, in that it is or may be >>> >> inconsistent >> >>> with what the authors were looking at during deposition"? >>> >>>> How about "Warning: the R-factor calculated for this map differs >>>> >>> significantly from the published R-factor"? >>> >>>> >>>> Then we can discuss what is significant ;-) >>>> >>>> Luca >>>> >>>> Luca Pellegrini >>>> Department of Biochemistry >>>> University of Cambridge >>>> 80 Tennis Court Road >>>> Cambridge CB2 1GA - UK >>>> >>>> Email: lp...@cam.ac.uk >>>> Tel: 0044-1223-760469 >>>> Fax: 0044-1223-766002 >>>> Sanger building, room 3.59 >>>> >>> >>
