John Penniston wrote: > I'm still trying to get to the end of my clustering script. Your last > bit of advice got me further, but I've come up against another error > that I can't solve, an "Atom index is out of range " error. At first I > thought this occurred because the sequence was being patched with an > OXT, but I get exactly the same error even if I prevent that. Below are > my script and the last part of the log. Sorry to bother you so much!

This occurs because the 'cluster' routine reads in the restraints file, which 'model' previously wrote out. But because you've set MODEL_SEGMENT, you're only trying to cluster part of the models, so some of these restraints won't apply any more. Either remove MODEL_SEGMENT, or rewrite your restraints file before calling 'cluster'.

Ben Webb, Modeller Caretaker