[phenixbb] Selenocysteine

Pavel Afonine pafonine at lbl.gov
Wed Mar 30 01:30:28 PDT 2016


> 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?


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