Yun He wrote: > When we use Modeller to build model, the default model routine (automodel > class) seems only to check the improper chain breaks (the distance between > two adjacent CA atoms is larger than 8 Angstrom) of templates, but not check > the CA clashes of generated models. And the models sometimes have the CA > clashes problem. How could Modeller avoid such improper geometry? Add some > distance restraints by hand?
The test you describe is alignment.check(), and is a very simple test, so can be run before modeling. If you want to detect bad models (e.g. CA clashes) after the modeling is complete, then that's the realm of model assessment such as GA341 or DOPE. Generally speaking, CA clashes should be prevented by the stereochemical restraints (CHARMM force field) although your template distance restraints may clash with these. You may need to weaken the homology-derived restraints in these regions, or remove them entirely by deliberately misaligning your templates to the target.
Ben Webb, Modeller Caretaker