[Chimera-users] Protonation of selected atoms ?

Marek Maly marek.maly at ujep.cz
Thu Nov 28 05:44:39 PST 2013

Dear Eric and Elaine,

thank you very much for your help !

My request comes from the fact that depending e.g. on pH
in general just the certain percentage of protonable groups
is really protonated. This for sure holds for "synthetic" polymers
but perhaps also for proteins.

To adjust protonation states on proteins I am using H++ server
( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated
  software e.g. to calculate ionic state of the protonable groups taking  
in account pH, dielectric constants (internal/external), micro-environment
of the protonable groups etc. Unfortunately this tool seems to works  
"just" for the proteins
(not for example for synthetic polymers or other molecules).

So I appreciated the possibility to add hydrogens to the molecular  
structure in Chimera.

Both advices (Elain's and Eric's) might be used to achieve desired partial  
of the molecular structure using actual chimera possibilities however  
depending on the size of the structure and depending on the percentage of  
the protonation and depending on the eventual additional requirements  
regrading  distribution of the protons between different molecular residues
(e.g. those containing primary amines, those containing secondary amines  
those containing tertiary
amines ...) it might be still more or less "dirty" manual work.

So if may I suggest something for the future Chimera development, it would  
be perhaps the possibility
to protonate just the given percentage (e.g. with random distribution) of  
certain kind of protonable atoms (e.g. primary, secondary, tertiary amines  
, O atoms on COO groups ) which moreover belongs just to actually selected  
molecular part. Of course that regarding "steric clashes" etc. also the  
"non-selected" parts of the structure should be always considered in the  
process of protonation of the actually selected parts.

    Best wishes,


Dne Wed, 27 Nov 2013 20:18:58 +0100 Eric Pettersen <pett at cgl.ucsf.edu>  

> Hi Marek,
> 	You can do this with Build Structure.  With the nitrogens selected, go  
> to that tool's "Modify Structure" tab and do the following:
> 1) Change element to N
> 2) Change geometry to tetrahedral if it isn't already
> 3) Change bonds to 4
> 4) Change "Residue Name" option to "Leave unchanged"
> 5) Click Apply
> Normally using Build Structure would be suboptimal since hydrogen  
> placement would not consider H-bonding interactions, but for protonating  
> tertiary amines that consideration is moot.
> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> On Nov 27, 2013, at 7:24 AM, "Marek Maly" <marek.maly at ujep.cz> wrote:
>> Dear all,
>> I would like to protonate just several nitrogen atoms
>> (tertiary amines) of my hyperbranched polymer.
>> I tried Structure "Editing -> Add hydrogens"
>> but it protonised all my tertiary amines in the structure
>> ignoring the fact that only few of them were selected and considered for
>> protonation.
>> So is there any way how to protonate only selected N atoms ?
>> If not would be a good idea to add this possibility into Add Hydrogens
>> panel (function).
>> Thank you,
>>    Best wishes,
>>        Marek
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
>> http://www.opera.com/mail/
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