On Wed, Jul 17, 2013 at 5:50 AM, Vinushka Schalk <[email protected]>wrote:
> Hi,
>
> I'm a web developer who has been using JSmol since January for various
> graphical functionality on a molecular simulations website (visualizing
> point-mutations, building custom ligand molecules, etc.) I am currently
> trying to develop a visualizer for changing protonation states in a
> protein: JSmol loads a PDB-format file (with added hydrogens from
> OpenBabel) and is displayed to the left of a series of selection boxes with
> various protonation states for the residues in the protein displayed in the
> JSmol window. Changing the selection in the selection box for a given
> residue thus is supposed to change the protonation state of the "important"
> atom in that residue (NZ in a LYS/LSN, OE2 in a GLU/GLUP, etc.).
>
>
> While selecting the atom with these criteria works fine, and the assign
> atom ({}) Pl/Mi command targets the correct atom, the protonation states
> are somewhat different than expected. If I start with an O(1-), as is the
> case for GLU, Pl adds two hydrogens, and doing Mi on that same atom removes
> both hydrogens.
>
>
I'm missing what "PI" and "Mi" are.
> Other strange behavior is that when deprotonating or protonating NZ, the
> atom name changes to "N299". I know this functionality works on basic
> molecules, but why does it become problematic on proteins?
>
>
Is this something in OpenBabel?
> Is there any way to change this behavior (particularly the name-change)?
> Would it be plausible to "create" a hydrogen atom and connect it to this
> atom? Or would that be even more problematic? I just want to be able to
> keep the name and make proper protonation states.
>
>
It's somewhat problematic adding protons to proteins. Not certain Jmol will
handle that correctly.
> To be clear, I will not be using this for any calculations, this is a
> graphical aid only, so any inaccuracies as a result are fine.
>
Check to see if the PDB file has "alternate location" flags set. Perhaps
you can utilize those. (See PDB specs)
>
> I am using the protein 4dfr (with hydrogens added with OpenBabel's
> AddHydrogens() function from the python bindings, though the command line
> version should be the same), and using the following selections as test
> cases for protonation/deprotonation:
>
> 32.NZ and atomno < 1000 (LYS deprotonation into LSN)
> 17.OE2 and atomno < 1000 (GLU protonation into GLUP)
>
>
> -Vinushka Schalk
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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