[phenixbb] Selenocysteine
Pavel Afonine
pafonine at lbl.gov
Wed Mar 30 01:30:28 PDT 2016
Hi,
> How to add an unnatural amino acid (say OCS) at a position in the
> sequence and view it in PyMol, provided the protein structure (PDB
> file) is given? Is it correct to make changes in the PDB file itself,
> if Yes, then how should I do it?
at the risk of setting a bad example... If I had to do it myself I would
edit PDB file manually to mutate existing residue into OCS, then I would
run a quick geometry minimization to fix up geometry (that is likely to
be distorted due to manual editing). If OCS is this
elbow.where_is_that_cif_file OCS
then everything may just work fine. Otherwise you may want to provide a
CIF file for it.
I wonder if this kind of manipulation can be done in Coot?
Pavel
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