Usha Nair wrote:
Dear all,
I have been trying to manually build a loop into low resolution maps
(data between 18 and 2.85A) in coot. However, I find that coot messes up
the stereochemistry of my model.
"Stereochemisty" meaning... what, in this case? Perhaps you mean the
Ramachandran plot?
The traffic lights in newer versions are there to address this sort of
issue.
This despite the fact that the program
appears to be reading the refmac library for standard amino acids just
fine. The only untoward message I get is when I try to do geometry
analysis (under the validate menu). While I get the required plot, I get
a message saying no restraints were found. The whole message is given below.
No restraints found! [snip]
Presumably you have a ligand that does not have a full description in
the refmac library.
Whatever cif library you use to refine your ligand in Refmac should be
imported into Coot, and this problem will go away.
Should I use planar peptide restraints as well to sort this problem?
Planar peptide restraints are unrelated to finding restraints for a
ligand. However, there is a good chance that they will reduce the
damage to a Ramachandran plot. That being said, all Coots less than 0.5
do a poor job at maintaining good Ramachandran geometry.
I have tried Wincoot 0.3.3 and Coot for linux 0.1.1.
Those are old Coots - particularly the "linux" version.
Consider updating to 0.4.1 or (if adventurous) 0.5-pre.
Paul.
