James All great stuff.
Ø The individual crystals were not twinned (or at least I would be VERY surprised if they were) Can this be tested? The spots should show fringes around them corresponding to the shape transform of the nano-crystal. If twinned, the intensities of the fringes should be modified due to the contrast between the two types of domain for the particular reflection. If it worked, one would be equivalent to grinding up the crystal using the coherent beam. Probably difficult as would have to be done independently for each crystal. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton Sent: 10 February 2011 01:20 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser The twin fraction for REFMAC was exactly 0.5. The individual crystals were not twinned (or at least I would be VERY surprised if they were), but they do belong to the space group P63, and autoindexing will give you one of the two possible axis conventions at random. So, of the 15445 crystals that were merged, there were about ~7700 indexed one way and 7700 indexed the other way. It is hard to tell exactly. Mergeing the data "blindly" (which we did) will result in a "twinned data set" where each merged h,k,l has an equal contribution from k,h,-l. This was all discussed in the data processing paper PMID: 20389587. Obviously, there are a number of things you can think of for resolving this indexing ambiguity and removing the "twinning effect", and in fact, this is what I thought was really cool about this particular kind of data collection and why I encouraged the people doing all the work (the other 87 authors) to go ahead with a "twinnable" space group. On the first pass, you can just take advantage of TWIN refinement in REFMAC, but in the future, when the indexing improves (probably using post-refinement) it may be possible to de-twin a crystal system that actually suffers from "real" twinning. That is, a "twin domain" cannot be smaller than a mosaic block (otherwise the h,k,l and -k,h,-l structure factors would add as phased Fs, not |F|^2). So, since nanocrystals are essentially single mosaic blocks (smaller than the coherence length of the beam), you could take your twinned crystals and either grind them up or re-optimize for smaller crystals (counterintuitive!), and then resolve the twin domains "manually". Sort of like Louis Pasteur and his tartaric acid crystals. Anyway, I thought that was a cool idea, but like so many other cool things, it had to be cut from the Nature paper. Admittedly, the problem has not actually been solved yet. This is why we used REFMAC in TWIN mode. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 3:29 PM, Jon Schuermann <schue...@anl.gov> 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." > >
