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Hi Weikai,
Q1
If you give the keyword SOLVENT the mask is automatically calculated
at updated at each refinement cycle. Scaling is controlled by the
keywords BULK or SIMPLE as described in the manual.
In version 5.3 of the program it is possible to use dummy atoms for
mask calculation that are not used during actual refinement. How to
use this option (and other new options) will (soon) appear first on
the web page http://www.ysbl.york.ac.uk/refmac/latest_refmac.html
from which the latest Refmac versions can be downloaded.
Q2
The bulk solvent correction in Refmac follows what is called the
'flat model' in the paper (a good paper to read in my opinion)
Jiang JS, Brunger AT.
Protein hydration observed by X-ray diffraction. Solvation properties
of penicillopepsin and neuraminidase crystal structures.
J Mol Biol. 1994 Oct 14;243(1):100-15.
As the Refmac bulk solvent correction did not really contain new
science we never published it. The few things that are important from
the user's point of view are in the manual. We've never done
comparative tests with CNS and our tests at the time were done on
data always higher that 3.0-3.5 A resolution.
Roberto
On 18 May 2006, at 20:23, [EMAIL PROTECTED] wrote:
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Hi All:
I have two questions for the bulk solvent model:
1. Maybe I missed this in reading the manual, but in Refmac is
there a
way of inputting an mask to define the bulk solvent? Or it is
always done
automatically using the keyword SOLVENT?
2. Is the bulk solvent model in Refmac somehow different from that in
CNS? For one of my low resolution data to 7A, the bulk solvent
model in
Refmac seems to behave much better than that in CNS. I only use rigid
body refinement and there is no TLS refinement in Refmac. So in this
case, maybe the major difference of R factor using these two programs
would come from the bulk solvent models (maybe also the scaling of
Fc to
Fobs, or maximum likelyhood, etc.?). Anyway the R factors differ
by 10%
using the two different programs (40% in CNS vs. 30% in Refmac)
when both
have a bulk solvent model. If I turn off bulk solvent estimation
in CNS,
the R factor drops by 5% (i.e. now R=35% in CNS).
Regards,
Weikai
---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail [EMAIL PROTECTED]
