Re: [modeller_usage] question about restraint violations

On 10/19/10 4:53 PM, Song, Hyundeok (songhk) wrote: > I generated some protein by Modeller. > When I checked the log file, I found a lot of restraint violations. > I have a question. > How can I remove restrain violations ?

Restraint violations, particularly of the distance restraints, tend to indicate either a poor choice of template (e.g. low coverage or low sequence identity) or an optimizer failure. In the latter case, simply build more models and pick the best one. In the former case, look for better templates.

Ben Webb, Modeller Caretaker