I performed DEN-refinement with CNS using the same data and starting model, and obtained similar "twinned" R values and maps. The twin fraction is 0.5.
Axel On Feb 9, 2011, at 3:29 PM, Jon Schuermann wrote: > According to the paper, the data was refined in REFMAC in 'twin mode' which, > I believe, calculates the R-factor using a non-conventional R-factor > equation which usually lower than the conventional R-factor. I believe this > is dependent on the twin fraction which wasn't mentioned in the paper (or > supplementary info) unless I missed it. > > Jon > > -- > Jonathan P. Schuermann, Ph. D. > Beamline Scientist > NE-CAT, Building 436E > Advanced Photon Source (APS) > Argonne National Laboratory > 9700 South Cass Avenue > Argonne, IL 60439 > > email: schue...@anl.gov > Tel: (630) 252-0682 > Fax: (630) 252-0687 > > > On 02/09/2011 05:11 PM, James Holton wrote: >> >> This was "molecular replacement" from 1jb0, so the phases came from the >> model. Probably more properly called "direct refinement" since all we did >> was a few cycles of rigid body. Personally, I was quite impressed by how >> good the R factors were, all things considered. >> >> -James Holton >> MAD Scientist >> >> On Wed, Feb 9, 2011 at 2:56 PM, Bernhard Rupp (Hofkristallrat a.D.) >> <hofkristall...@gmail.com> wrote: >> Any idea where then phases came from? >> BR >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas >> Juettemann >> Sent: Wednesday, February 09, 2011 12:16 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] First images of proteins and viruses caught with an >> X-ray laser >> >> Thank you for clarifying this James. Those details are indeed often >> lost/misinterpreted when the paper is discussed in journal club, so your >> comment was especially helpful. >> >> Best wishes, >> Thomas >> >> On Wed, Feb 9, 2011 at 20:38, James Holton <jmhol...@lbl.gov> wrote: >> > >> > As one of the people involved (I'm author #74 out of 88 on PMID >> > 21293373), I can tell you that about half of the three million >> > snapshots were blank, but we wanted to be honest about the number that >> > were collected, as well as the "minimum" number that were needed to >> > get a useful data set. The blank images were on purpose, since the >> > nanocrystals were diluted so that there would be relatively few >> > double-hits. As many of you know, multiple lattices crash autoindexing >> algorithms! >> > >> > Whether or not a blank image or a failed autoindexing run qualifies as >> > "conforming to our existing model" or not I suppose is a matter of >> > semantics. But yes, I suppose some details do get lost between the >> > actual work and the press release! >> > >> > In case anyone wants to look at the data, it has been deposited in the >> > PDB under 3PCQ, and the detailed processing methods published under PMID: >> > 20389587. >> > >> > -James Holton >> > MAD Scientist >> > >> > On 2/9/2011 10:38 AM, Thomas Juettemann wrote: >> >> >> >> http://www.nanowerk.com/news/newsid=20045.php >> >> >> >> http://home.slac.stanford.edu/pressreleases/2011/20110202.htm >> >> >> >> I think it is pretty exciting, although they only take the few >> >> datasets that conform to their existing model: >> >> >> >> "The team combined 10,000 of the three million snapshots they took to >> >> come up with a good match for the known molecular structure of >> >> Photosystem I." >> > >> > >> >
