In this case, editing the pdb file is probably the best approach. However, my favorite approach is "Validate" "Difference Map Peaks". By pressing "." (next peak) or "," (previous peak), one can quickly go through all problems (red density) or unexplained peaks (green density). The pointer will be automatically set in the peak center, so all one has to do is to use the "add atom" or "get monomer" option to add something at the peak position.
Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Remie Fawaz-Touma Gesendet: Mittwoch, 19. März 2014 02:59 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Add an atom in Coot 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 mjvanra...@cnb.csic.es: "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
