On 04/11/14 20:35, Jan Stransky wrote:
Hi Dorothy,
this dashed lines represent links.
Yes - you can tell this because they are drawn in the same colours as
the molecule with the half-bond colour scheme.
You can delete them in PDB-file, look for keywords LINK and LINKER.
LINK and LINKR.
In coot you can create them via tool in menu.
However its creation after Real Space Refinemnet or Regularize zone
looks to me as a bug.
Not a bug, which is to say, the program is working as expected. The RSR
that you get from clicking on the toolbar button is simple-minded in its
residue selection.
For Coot to take into account the links, one should first use an mmCIF
file that defines the link and second, use Sphere Refine - which does a
better job at residue selection than does standard "blue circle button"
refine.
Paul.
