Lella Sana wrote: > how could I carry out GA341 assessment on a model not produced by > MODELLER but by an ab initio method? > I'm using MODELLER 9v2.

The example given at http://salilab.org/modeller/9v4/manual/node188.html should work for any PDB file - not just one produced by Modeller. But, as described in the manual, the sequence identity is a parameter used in the GA341 score, so you need to provide that. For models that are not homology-derived, you'll have to make a reasonable guess at some "equivalent sequence identity" or use a different assessment method, such as DOPE.

Ben Webb, Modeller Caretaker