crystal orientation during data collection

From: yanwu huo
Date: 17 November 2011 22:00

Hi,
I worked on a crystal sensitive to radiation damage, So I need to merge many crystal to obtain complete dataset, Does anyone know such program that can tell crystal orientation after first frame exposure.
Thank you in advance.


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Thank you very much and all the best,

Yanwu Huo
Postdoctoral Associate

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From: Jim Pflugrath

All the currently used diffraction image processing programs can tell the crystal orientation from a single diffraction image.

Some programs like d*TREK can calculate new orientations for the crystal if the crystal is mounted on a reasonable goniometer such as the Rigaku Kappa goniostat or the Rigaku quarter-chi goniostat. :)  And the strategy program in d*TREK can use a list of previously collected and/or processed Bragg reflections to make sure that the new strategy fills in the missing parts of reciprocal space.

Jim

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From: Frank Murphy

Yanwu,

I surmise from your question that you are inquiring how to go about collecting from many crystals optimally. Merging data ex post facto is a totally different kettle of fish.

In my opinion, the most robust way to go about this is to use a kappa goniometer as Jim suggested (I am most familiar with the MK3). Since you intend to collect from many crystals, align the first and all subsequent crystals to the same easily attainable (or seemingly so) orientation, and then collect the sweep suggested by your data collection strategy program of choice.

To achieve this at NE-CAT, we have a GUI-based system that used STAC for orientation determination and BEST for strategy generation. As Jim suggested, more options than STAC exist.

If anyone is unable to get to a kappa goniometer, they can employ Mosflm or XDS (Xplan) to generate strategies for data collection from a crystal taking into account previously collected data. This is not nearly as robust a solution, but is a workable substitute (and also automated at NE-CAT).

I know there are other ways to achieve similar results, but I have suggested the methods I am most familiar with...

Yours,

Frank Murphy

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From: Frank von Delft

I believe you achieve completeness more quickly (fewer crystals) if you just take random orientations.  At least, that's what I learnt from Dave Stuart.
phx

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From: Mark J van Raaij

I don't think one can generalise that much.
In the Stuart case of BTV, only 1-3 useful images per crystal could be obtained if I remember correctly - so there the random strategy orientation makes sense. I.e. if you collect one image and then wait until the orientation and strategy is calculated, the crystal is probably already dead.
For projects where more images can be collected from a single crystal, I would think it makes more sense to use the strategy options described (like was done for F1-ATPase).
Another thing to keep in mind is how to achieve this random orientation, one can not always count on the crystal orienting randomly in a loop, i.e. many crystals have preferred orientations when mounted...and one tends to mount the loop on the goniometer the same way each time. So one would have to use "random" starting phis.

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas

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From: Harry Powell

Hi Frank

I believe (at least part of) the key to the 30S ribosome structure was being able to orient the crystals carefully and collect the data accordingly - see Brodersen et al, Acta Cryst. (2003). D59, 2044-2050

Completeness, while important, ain't everything.

Harry
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Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH

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From: Sanishvili, Ruslan

Depending on the crystal shape, "random orientation" is not always random. Many crystals have tendencies of sitting themselves in one predominant posture in the mount. Compounding this, many experimenters have tendencies of rotating the mount into a specific orientation when centering. Then crystal orientation ends up being not random at all, so understanding it's true orientation as my neighbor Frank suggests can be highly beneficial.

Cheers,

N.

 

Ruslan Sanishvili (Nukri), Ph.D.

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From: Jacob Keller


Generally speaking, don't we agree that "planned" or "rational" is
better than "random?" (Having trouble understanding the argument for
randomness here...)

Jacob

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Jacob Pearson Keller
Northwestern University

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From: Sandor Brockhauser

I would interpret "random" as aimed to be uniformly distributed, or highly diverse,... continuing this chain of definitions and having a precise kappa goniometer in hand, we can easily arrive to a "planned" strategy to follow. Certainly, if you can get only a few frames per xtal - Frank (vD), do you remember when we had a project like this together- you may not have the luxury of being able to afford to loose a complete frame(s) just to get to know the initial orientation of the crystal(s).

In any case, I am happy to learn that our solution 'STAC' is useful for the community. Actually, we are organising an International Kappa Workgroup Meeting in Berlin on Nov 28-29. Registration is normally over, but if there is anyone interested in learning more about current developments for sample reorintation on synchrotron beamlines, please contact us directly and join us in Berlin.
http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/kappa-meeting/index_en.html

Sandor