I would assume that the wrong chiralities were introduced during building.
It is not very hard to change chiral centers around if you're dragging atoms
around in and out of density...
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Dale
Tronrud
Se
First you should look into why your chiral centers flipped. In
my experience the most common cause is that the neighboring peptide
bond needs to be flipped.
If you just want to flip a chiral center in Coot, I think the
easiest way is to "real space refine" the residue and before accepting
Did you set the weight (X-ray.vs.Geom.) too high? In principle, at
3A a relatively smaller weight than default (0.3?) may be used.
On Aug 2, 2008, at 8:39 AM, Yusuf Akhter wrote:
Hi Everybody,
I am refining structure of a protein at 3 Angstrom. I am doing
model building in
Coot.
After s
The easiest (albeit by far not the simplest!) option is to mutate the
offending amino acid to Gly, then back to what it should be.
Alternatively you could use a script to accomplish the same, but if you only
messed up 1 or 2 residues, the above is easier.
Artem
-Original Message-
From: C
Hi Everybody,
I am refining structure of a protein at 3 Angstrom. I am doing model building in
Coot.
After several rounds of refinement using Refmac when I tried to run PROCHECK on
my partially build model I found that some of the residues are D-amino acids.
How to change these D-amino acids to L
Hi Everybody,
I am refining structure of a protein at 3 Angstrom. I am doing model building in
Coot.
After several rounds of refinement using Refmac when I tried to run PROCHECK on
my partially build model I found that some of the residues are D-amino acids.
How to change these D-amino acids to L
