Hi Dan,
You're missing a slash. You have:
PyMOL.exe -qc mutate.py -- digly.pdb digly A/2 ASN
where you should have
PyMOL.exe -qc mutate.py -- digly.pdb digly A/2/ ASN
When the residue is properly selected you'll see this:
Selected!
Mutagenesis: 4 rotamers loaded.
ExecutiveRMS: RMS = 0.083 (4 to 4 atoms)
Mutagenesis: 12 rotamers loaded.
where the RMS will change based on your residues.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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