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On Dec 2, 2005, at 10:21, Tim Gruene wrote:
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Hello,
you have to lower the weight between crystrallographic and geometric
data.
That is the matrix keyword. I think the default is 0.3, which in my
experience is much to high at the beginning of refinement.
Its completely resolution dependent.
MATRIX 0.3 is correct for about 2.0 A.
for 2.5 A you sometimes need 0.05.
for 1.5 A, 0.5-0.7 tends to be OK.
I would suggest to aim for 1-2 distances rms between 0.015-0.020 and
angles about 1.5 degrees.
You can try
setting it to AUTO instead of a number and let refmac figure it out for
you. If the protein is still distorted, lower the value until the
geometric statistics look reasonable.
AUTO is great as a rough guess - in my experience towards the end of
refinement you better tune yourself.
Tassos
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Fri, 2 Dec 2005, [gb2312] Àî°º wrote:
I used refmac5 to refine a structure out from MR. But it seems
the geometric parameters of the output model are really bad,
only 50% residues are in core region of Ramachandrans plot, all
output from procheck are not good, Rfree value of the model is about
45%. Can someone give any suggestions? Is there any special
parameters needed when the refinement is on some initial moder?
I didn't met such problem on models that are almost correct.
Any help are thankful!
Yuhe Liang
