Hi Paul,
Thanks for your help on this!
I've finished sketching up 2AP in sketcher. However, I'm sure that
several of the bond lengths in the nucleotide base are now non-ideal.
Is there a way to idealize them before importing them into coot?
Thanks! and all the best,
--Buz
On Mar 28, 2009, at 8:37 AM, Paul Emsley wrote:
Buz Barstow wrote:
Dear All,
I'd like to add substitute a natural base (adenine) for a non-
natural base (2-aminopurine), in a molecular model of an RNA
molecule.
I'd like to do this with CCP4 and Coot. Could I ask for some help
please?
The "CCP4 way" would be to use sketcher and search for
aminopurines. You will find 2,6-diaminopurine (1AP). Load this up
and delete the 6-amino group to convert to 2-aminopurine. Save the
coordinates and dictionary (give it a new name).
Fire up coot and File -> Import CIF dictionary...
Centre on the residue you want to substitute
Extensions -> Modelling -> Replace residue -> 1AP (or whatever you
called it).
(If you have a map loaded when you do this, it will try to fit to
that as a final step)
Paul.
