Dear Jacob,
That should indeed be our ultimate goal: refining against the image data
rather than against process data. This would require a good model for
the crystal, mosaicity being an important parameter in this, and for the
internal variation in the molecular structure. Modelling the Bragg spots
is what we do currently wth EVAL. James Holton is doing also this with
nanoBragg. Unfortunately we would also have to simulate solvent rings etc.
Best wishes,
Loes
On 07/25/19 19:07, Keller, Jacob wrote:
>>It would seem to me that an important issue is also: do get all
information out of our diffraction data? By integrating the Bragg
peaks we usually neglect the diffuse scattering that could potentially
contain additional (dynamic) structural information. This can be
cloudy diffuse scattering hidden in the background but also diffuse
streaks that contain information on packing disorder and reveals
intrinsic interactions in the crystal.
Along these lines, and taking a page from you also, how about
“crystallographic model refinement as image-faking?” Metrics of the
goodness of a particular refinement could simply be some measure of
the correlation between predicted vs. measured images. I have seen
some of this done with diffuse scattering, but why not with the whole
thing, including intensity and shape of Bragg peaks, solvent rings,
etc? Maybe instead of doing the multiple steps of (indexing,
integration, scaling, solving…) all of this could be refined as one?
Processing parameters like moscaicity [sic] etc would now be part of
the final model…?
JPK
Loes Kroon-Batenburg
On 07/15/19 21:44, Holton, James M wrote:
Hello folks,
I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020). This meeting will focus on the biggest challenges currently
faced by structural biologists, and I mean actual real-world
challenges. As much as possible, these challenges will take the
form of
friendly competitions with defined parameters, data, a scoring
system,
and "winners", to be established along with other unpublished results
only at the meeting, as is tradition at GRCs.
But what are the principle challenges in biological structure
determination today? I of course have my own ideas, but I feel
like I'm
forgetting something. Obvious choices are:
1) getting crystals to diffract better
2) building models into low-resolution maps (after failing at #1)
3) telling if a ligand is really there or not
4) the phase problem (dealing with weak signal, twinning and
pseudotranslation)
5) what does "resolution" really mean?
6) why are macromolecular R factors so much higher than
small-molecule ones?
7) what is the best way to process serial crystallography data?
8) how should one deal with non-isomorphism in multi-crystal methods?
9) what is the "structure" of something that won't sit still?
What am I missing? Is industry facing different problems than
academics? Are there specific challenges facing electron-based
techniques? If so, could the combined strength of all the world's
methods developers solve them? I'm interested in hearing the
voice of
this community. On or off-list is fine.
-James Holton
MAD Scientist
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Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
E-mail : l.m.j.kroon-batenb...@uu.nl <mailto:l.m.j.kroon-batenb...@uu.nl>
phone : +31-30-2532865
fax : +31-30-2533940
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__________________________________________
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
E-mail : l.m.j.kroon-batenb...@uu.nl
phone : +31-30-2532865
fax : +31-30-2533940
__________________________________________
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