Re: [modeller_usage] Questions about alignment and stereo clashes

On 3/30/20 11:15 AM, Li,Haoxi wrote: > 1. Am I able to use the sequence alignment from external sources, > like Blast?

Of course. Modeller doesn't care where the alignment comes from, as long as it's in the correct format.

> 2. When the model was built, I found many stereo clashes in the > structure. Is this normal? Is there any way that I can fix the stereo > clashes?

Most likely this is due to a poor alignment. But you would need to look at the clashes in a PDB viewer to see what's going on.

Ben Webb, Modeller Caretaker