Ah, I see. definitely odd. I'm sure the hydrogen addition to proteins needs
some work -- this was not designed with proteins in mind. I can look into
that. Please send [email protected] the pdb file that comes from
OpenBabel.
Have you tried
set pdbAddHydrogens
load xxx.pdb
? There's no pH dependence there -- all amines will be protonated and all
carboxyls will be deprotonated. Histidine residues will get two protons.
Bob
On Thu, Jul 18, 2013 at 5:01 PM, 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.
> "Pl" and "Mi" are Jmol's stand-ins for "increase charge on this atom" and
> "decrease charge on this atom" (I believe it uses assumed valences for
> this). It's documented in the "assign atom" command, at least in
> CHANGES.TXT. It's also used in graphical (mouse-driven) set picking, as
> seen for example here (clicking +1/-1 triggers the command set
> picking_assignatom Pl/Mi):
>
> http://dgu.ki.ku.dk/molcalc/#
>
> The expected behavior would be to add or remove 1 hydrogen, but on a
> protein it can add or remove two at a time.
>
>
>
>
> >> 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?
>
> No. The original PDB has the atom name "NZ", and after OpenBabel its name
> remains "NZ". It is only after attempting to deprotonate it with the Jmol
> command "assign atom ({selected}) Mi" that its name is changed to N299. I
> don't really know why it happens.
>
>
>
>
> >> 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)
>
> As far as I know, it doesn't. The PDB files we get (which are from RCSB)
> usually leave that field blank.
>
> However I will note that when OpenBabel is called to "create" hydrogens on
> the molecule, the element symbol in fields 77-78 changes from, e.g., "N" to
> "N1+", or "O" to "O1-" (the second ones violating PDB specs). I'm not sure
> how important this would be.
>
>
>
>
> >>
> >>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<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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--
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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