Hi, Sometimes when I move a molecule using an SSM alignment the molecule looks fine in coot, but when saved and subsequently read into pymol has all kinds of problems.
The problem is in the connect lines at the bottom of the file - if you remove them then pymol reads the file just fine. You could say that this is a pymol read problem, But I'm going to suggest that this is a coot write problem. These connect lines must mean something and whatever they mean it's not the same after you rotate the coordinates. So, maybe coot has to rewrite the connect files or leave them out? Heidi
