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

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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 <mailto:hofkristall...@gmail.com>> wrote:

    Any idea where then phases came from?
    BR

    -----Original Message-----
    From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
    <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Thomas
    Juettemann
    Sent: Wednesday, February 09, 2011 12:16 PM
    To: CCP4BB@JISCMAIL.AC.UK <mailto: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
    <mailto: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."
    >
    >




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