I do not think I made myself clear... WEIGH AUTO does not work very well (and Clemens's attempt to apply a similar method to weigh the X-ray terms in autoBUSTER) because all the types of geometrical restraints (DIST, ANGL, PLAN, CHIR, NONB, etc...) are scaled by the same factor for all resolutions, with rmsd for 1-2 bonds being used as an indicator of how well we balance the X-ray terms with the geometrical ones (in the parameter matrix).
This indeed can lead to larger bond rmsd for high-resolution structures (competition between DIST restraints with stronger X-ray terms), and very small ones for low-resolution data (no competition, DIST wins!).
I am suggesting applying different scale factors for different types of geometrical restraints, depending on the resolution to have a more realistic distribution of the deviations from "ideal" values for different types of geometrical features.
Tadeusz
| "Roberto Steiner"
<[EMAIL PROTECTED]>
23-Aug-2006 12:05 |
|
Hi Tadeusz
Of course, one can adjust weights of individual types of restraints (does anybody these days?), but It would be nice to have an automatic weighing scheme in REFMAC, which would deal with the different needs for restraints at different resolution ranges...
You can try
WEIG AUTO
The option is not yet available through the interface (I think). I usually modify the CCP4i-generated refmac script with Run&View Com File.
Alternatively, you can just have a one-line file with the above command and give the name of that file in the Developers option.
Roberto.
Tadeusz
| "P.R. Evans"
<[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED] 23-Aug-2006 10:17 |
|
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When I've done searches of the CCDC small molecule database for molecular
fragments, the rmsd of bond lengths has come out in the range 0.02 - 0.03A.
These deviations between different structures are of course larger than the
estimate rmsd within a single structure, which I think are the number
around 0.014A quoted earlier in this thread, and probably give a reasonable
estimate of the uncertainty.
I usually try to adjust matrix weight to give rmsd bonds around 0.02A
Phil
---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
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King's College London
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