Hi everyone, Sorry for posting my replies to the list; I hope this is all generally useful.
Firstly, the bug: the obvious cause is if the line "if ss == currentType:" is never true. In that case, it is making a list of one-residue sses, with, as Tsjerk correctly pointed out, the default end of -1. Secondly, the root cause /may/ be that the name "ss" is used for both the loop variable and the function name. I can't see why else it fails. It works fine for me on MacPymol 1.0r2, but something is different. Thirdly, the way I run these kinds of commands is to save them as text files in a directory (~/development/pymol as it happens) and them in the .pymolrc file, I have lines like "run ~/development/pymol/motif.py" to add commands. However, copy/paste seems to work for me also. gilleain
