Thanks to all who answered. In fact my question is as below: how do you place the pointer if there is no bond there? (just density) I am trying to connect 2 sugars creating 2 bonds to one oxygen that I have to add (oxygen does not exist now).
and I got the answer from [email protected]: "in that case I would just add it by hand in the pdb file using a text editor, guessing the values for the coordinates by interpolating between the two atoms it should be in between of. Then do a "regularize zone" and/or real space refinement to make sure geometry is ok.” Remie
