5.23 Add Terminal Residue

This creates a new residue at the C or N terminal extension of the residue clicked by fitting to the map. \phi,\psi angle pairs are selected at random based on the Ramachandran plot probability (for a generic residue) and fitted to the density. By default there are 100 trials. It is possible that a wrong position will be selected for the terminal residue and if so, you can reject this fit and try again with Fit Terminal Residue ¹. Each of the trial positions are scored according to their fit to the map ² and the best one selected. It is probably a good idea to run “Refine Zone” on these new residues.

If you use the Extensions (Dock Sequence... -> Associate Sequence with Model) to apply a PIR sequence file to a model then Add Terminal Residue will use the sequence alignment to determine the residue type of the added residue.

Sometimes, particularly with low resolution maps, the added terminal residue will wander off to somewhere inappropriate. This can be addressed in a number of ways:

1. (set-terminal-residue-do-rigid-body-refine 0) will disable rigid body fitting of the terminal residue fragment for each trial residue position (the default is 1 (on)) - this may help if the search does not provide good results.
2. to anneal the newly added residue back to the clicked residue (no matter where it ended up being positioned): (set-add-terminal-residue-do-post-refine 1)
3. (set-add-terminal-residue-n-phi-psi-trials 200) will change the number of trials (default is 100). This is useful if you think that Coot needs to search harder to find a good solution to the positioning of the next residue.