On 04/11/14 20:35, Jan Stransky wrote:

[log in to unmask]" type="cite"> 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.

[log in to unmask]" type="cite">You can delete them in PDB-file, look for keywords LINK and LINKER.

LINK and LINKR.

[log in to unmask]" type="cite"> 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.