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
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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."
>
>
