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.
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 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.
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.
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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