Re: [ccp4bb]: dodgy indexing

[Mischa Machius <Mischa.Machius@UTSouthwestern.edu>]

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Hi Lauris,

>I'm trying to index a data set with denzo. The problem is with
>mosaicity-it looks about 1 but at this value it misses out some low
>resolution spots and seems to overfit for the number of spots at high
>resolution. Thought it might be misindexed but did a direct beam shot
>and the beam values look about right. It manages to autoindex it fine
>and the chi values are also fine.
>Lauris

What you describe is perfectly normal behavior (for denzo, anyway). I 
understand that it is difficult to model some reflections at low 
angle that are spread out over many frames. They are often ignored. 
Use as many frames as you want for integration of your data (HKL2000, 
or denzo_3d). This gives you a very good estimate for the mosaicity 
right during integration. If you are just using Denzo, integrate your 
data, then scale them and re-integrate using the mosaicity value that 
Scalepack gives you (add about 0.2). Keep in mind that the mosaicity 
can change depending on crystal orientation, radiation damage, etc., 
that's why it is best to refine the mosaicity during integration in 
the first place.

In any case, there will be reflections that won't be "predicted", for 
various reasons. The most common is that they don't belong to the 
main lattice (freezing artifacts, satellite crystals) or they come 
from a different crystal altogether (salt). Furthermore, mosaicity, 
or the sum of parameters that most integration programs call 
"mosaicity", seems to be resolution dependent. As far as I know, no 
program can model this in a satisfactory way. Don't worry about the 
few unpredicted reflections. It seems that your data processing is 
just fine.


Cheers,

Mischa

-- 
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Mischa Machius, PhD
Assistant Professor
University of Texas Southwestern Medical Center
Department of Biochemistry
5323 Harry Hines Blvd.                                Tel: +1 214 648 9760
L4.250                                                Fax: +1 214 648 8954
Dallas, TX 75390-9038, U.S.A.     Email: Mischa.Machius@UTSouthwestern.edu
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