On 12/04/17 00:31, Roger Shek wrote:
> Does anyone know why Coot is placing ligand outside the electron
> density where my model is built. I have put the cursor to where I want
> it to search, but when it fits, it places the ligand in the equivalent
> spot, but outside the model and not where the cursor was?
By "cursor" do yo mean the rotation centre marker? Let's imagine that
you do. Coot will place the ligand close to the centre of the screen if
you activate the "Right Here" button. If you don't do so, it will
search the whole asymmetric unit and try to map the model position back
to somewhere close to the protein. This can be slightly hit and miss
(depending on the position of the protein in relation to the asymmetric
unit). If you want to change the position of the fitted ligand to a
symmetry related one, you can (1) centre on the symmetry-related ligand
(2) use Extensions -> Modelling -> Symm Shift Reference Chain Here.
Paul.
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