You're going to have to help me find that. I'm just not seeing it. Please
describe exactly what you do.
On Fri, Jul 19, 2013 at 12:06 PM, Vinushka Schalk
<stefan.schal...@ncf.edu>wrote:
> The functions you gave work wonderfully and the protonation/deprotonation
> works appropriately now, at least on a functional level. However, I am
> still encountering a problem where after the protonation/deprotonation the
> atom's name changes from "NZ" to something like "N175" (where 175 is the
> atom number of the nitrogen in the PDB file). Is there any way to stop this
> automatic renaming outside of forcing it back into place with
> {selection}.name = "NZ"?
>
> A similar bug happens with HIS, except the names are changed from the
> "CD2,ND1,CE1,NE2" in the PDB file to names with atom numbers like "C502",
> before I do any charge changes. This is probably happening due to set
> pdbaddhydrogens.
>
> The OD2 and OE2 of aspartic and glutamic acid, however, do not change
> names and work perfectly, the protonation now only occurs once.
>
> It would be nice to have the names because I want to be able to rely on
> the fact that NZ or CD2 is labeled as such to change their states in a much
> more generic fashion.
>
> -Vinushka Schalk
>
>
> On Fri, Jul 19, 2013 at 8:37 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> That should have read:
>>
>>
>> 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
>>
>> then Jmol will assign multiple bonding correctly for all groups
>> (including ligands) and then will properly place H atoms for roughly pH 7.
>>
>> [but, as I said, [O](C=O) will not have a 1- charge due to that bug]
>>
>> Bob
>>
>>
>> On Fri, Jul 19, 2013 at 7:34 AM, Robert Hanson <hans...@stolaf.edu>wrote:
>>
>>> 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 <hans...@stolaf.edu>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 hans...@stolaf.edu 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 <
>>>> stefan.schal...@ncf.edu> 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
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> ------------------------------
>>>>> >------------------------------------------------
>>>>> >> See everything from the browser to the database with AppDynamics
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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
>>>
>>>
>>
>>
>> --
>> 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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>>
>
>
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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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