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I am already using a matrix weight of 0.03. Is that significant to use a
lower value? How low can I go?
Thanks,
Mario Sanches
Mark A. White wrote:
On Tue, 2006-08-22 at 14:44 -0300, Mario Sanches wrote:
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Dear All,
I am on the final stage of refinement and I am making sure, on coot,
that the residues are in the allowed regions of the Ramachandran Plot.
The problem is that, after Refmac, those residues are thrown back on the
disallowed regions.
This a low resolution structure (3.35A). I am using a matrix weight
which renders a RMSD bond of 0.02A.
1) At 3.35 A resolution your bond rmsd should be around 0.005 A
(depending on your solvent content).
2) Use a lower matrix weight in the refinement.
3) Phi and Psi are poorly determined at low resolution.
Since it is very low resolution, I
thought it would be a good idea to keep all residues in the allowed
regions. Is there any way to tell Refmac to keep it there?
Thank you in advance,
Mario Sanches
Sincerely yours,
Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Fax. (409) 747-4745
mailto://[EMAIL PROTECTED]
http://xray.utmb.edu
http://xray.utmb.edu/~white
