Hi,

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 elbow.

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

--

Ryan K. Spencer, Ph.D.

Postdoctoral Researcher

Hochbaum Laboratory

Chemical Engineering & Material Sciences

University of California, Irvine

From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine
Sent: Wednesday, March 30, 2016 1:30 AM
To: Shilpa Janarthanan <[email protected]>; [email protected]
Subject: Re: [phenixbb] Selenocysteine

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