I think the problem is that your formal charges are not being set up for
proteins. If you do not have multiple bonds, then there is no way for Jmol
to set the correct formal charges. If you use
set pdbaddhydrogens
load xxx.pdb
I took a look at OpenBabel, converting 1blu with adding hydrogens at pH
7.0. If you take a look there, it pretty well messed up LYS74. Whatever
OpenBabel is doing, it doesn't seem to have any real sense what it is
doing. There are carbon atoms that are connected to only 2 atoms, and there
are prolines that are sp2-hybridized. Also, I note that Jmol cannot read
the groups properly for those OpenBabel files anyway because each group's
atoms are not contiguous in the file.
That said, there is a bug in Jmol's PDB add hydrogen method in that
carboxyl oxygens are not given a 1- formal charge. I've corrected the bug,
but you could do a work around by issuing
{_O and connected(1, single)}.formalCharge = -1
until I get that released.
On Fri, Jul 19, 2013 at 3:51 AM, Robert Hanson <[email protected]> wrote:
> 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
>> >-------------- next part --------------
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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
>
>
--
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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