Re: [ccp4bb]: Denzo v. Mosflm

[Phil Jeffrey <phil@xray2.mskcc.org>]

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On Thu, 16 Jan 2003, James Stroud wrote:

> But my completeness in the outer bins is disasterous:
>
     <snip>

>    3.55  3.38   3.5   9.4  18.9  29.7  45.7  69.7  86.9   7.4   94.2
>    3.38  3.23   5.4  15.6  27.9  37.7  52.0  66.4  76.4   5.9   82.3
>    3.23  3.11   7.1  15.8  25.8  34.4  44.0  52.5  57.8   4.4   62.2
>    3.11  3.00   6.2  14.6  22.6  27.9  33.6  38.8  41.7   0.9   42.6
>  All hkl        3.1   7.7  13.3  18.5  26.5  39.8  58.2  27.3   85.5
>
> It seems like scalepack is tossing reflections. Is there a reason why? I
> picked these resolution limits by inspecting as denzo integrated. There did
> not appear to be a great number of reflections tossed during integration.
> This appears to be happening during scaling, so I don't believe it is
> overlap. Since I used denzo_3d, the fact that I have many partials (1.0
> degree oscillations) should not hurt, should it? Eg.:
>
>  type     good   intns   weak overlap  backgr others  total outside    tail
>                   ovfl                   prob
>  partials  461       0   2142       8       3     28   2642       1       0
>  whole      48       0    187       0       1      0    236       0
>  total     509       0   2329       8       4     28   2878       1

I'm assuming that Scalepack isn't throwing out a large # of reflections,
or that your mosaicity doesn't change much during postrefinement - the
usual sort of Scalepack mayhem.

In these situations, I always check the value of Profile Fitting Radius
used during Denzo. If I remember correctly, this dictates how far Denzo
looks for representative "strong spots" for generating spot profiles. I
tend to use 20-30. If the Profile Fitting Radius is too small, this can
manifest itself as a loss of the weaker high resolution data, especially
in cases where the data is anisotropic.

Just a guess.....

Phil
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| Phil Jeffrey                                  |                             |
| Crystallography Facility Manager              | If you lie to the compiler, |
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| phil@xray2.mskcc.org                          |     - Henry Spencer         |
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