[phenixbb] Selenocysteine

rspencer rspencer at uci.edu
Wed Mar 30 07:47:16 PDT 2016



A lot of the monomers are available in Coot and there are a couple different
ways to access them for either integrating into a structure or generating a
monomer pdb file to do some further minimizations and cif generation using


In Coot - To change a residue in a protein structure, select the residue of
interest and then 'Extensions' -> 'Modeling' -> 'Replace residue' . In the
window that pops up type OCS. This will automatically change whatever
residue you selected to OCS. 


To see/generate just the residue go to 'File' -> 'Search Monomer Library'
and enter CYSTEINESULFONIC ACID. This should return the OCS monomer. You can
then save that monomer as a pdb and generate a cif using elbow if the cif
file isn't already part of the phenix library. 


Hope that helps.






Ryan K. Spencer, Ph.D.

Postdoctoral Researcher

Hochbaum Laboratory

Chemical Engineering & Material Sciences

University of California, Irvine




From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Wednesday, March 30, 2016 1:30 AM
To: Shilpa Janarthanan <shilpa.janarthanan at gmail.com>;
phenixbb at phenix-online.org
Subject: Re: [phenixbb] Selenocysteine



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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