This is one of the reasons I love open-source:

On Thu, Jan 21, 2010 at 7:58 AM, David Hall <dwash59_2...@yahoo.com> wrote:
> So, I figured it would be nicer if I sent the author a patch instead of just 
> complaining, so I went to look at the code.

To answer your question, iterate and alter scan over the residues in
order.  (If you make updates to the sequence or IDs in the sequence
don't forget to issue the "sort" command.)   I ran into this exact
problem when I wrote CEalign--missing residues.  Using iterate/alter
over a selection should solve your problem.

Good luck, let me know if I can help you out.

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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