I am afraid that if this is happening you may have a problem of
interpretation. Even at 3.35A resolution, residues with good geometry
which fit the density will stay there.. It is quite easy to correct
Ramachandran plots by introducing strain into other parts of the
molecule, which refinement will then try to "correct".
Try the idealisation within REFMAC and see if that leaves your rebuilt
structure with good Ramachandran scores. That will try to fix other
strains you may have imposed..
Eleanor
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. 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
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