On 25/10/14 14:51, Kgosisejo, Oarabile wrote:
I am trying to fit cacodylate ion in my model using Coot but it does
not stay where I put it. The molecule breaks apart and some of its
components attach to the peptide residues. Due to this, phenix.refine
would not accept this as the input for refinement. Is there a way I
can make cacodylate ion stay in its electron density and refine my
structure with cacodylate ion?
Without details it's hard to know what to advise. As a general rule,
when reporting problems with Coot, I'd like to encourage the following:
The version of Coot being used
From where was it downloaded
What Coot said in the terminal from which it was started
Describe which buttons you clicked, keys you pressed or atoms you
selected so that we can reproduce the problem
Now, to clutch at straws... Are you sure that the map to which you are
refining is the map that you're looking at? Have you tried changing the
refinement weight factor to 6.0 or so?
Having said all that, the hydrogen atoms on CAC are incorrectly drawn in
Coot.
Paul.
