[Chimera-users] Add Hydrogens - non standard residue - protonation state

Subha Kalyaanamoorthy kalyaana at ualberta.ca
Thu Aug 18 16:28:02 PDT 2016

It did help!

Thanks a lot.

Best Regards,

On Thu, Aug 18, 2016 at 5:12 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Subha,
> Chimera makes its best guess as to the atom types in a nonstandard
> residue, using the bond lengths and angles. In this case it did not figure
> out the atom type you expected.  You would need to correct the atom type of
> that N atom to what you want before adding hydrogens and to do so, you
> would need to know its atom name (or serial number, or some way of
> specifying it in the command).  There is no general way to specify the net
> charge of a nonstandard residue in the addh command.
> The atom types in Chimera are described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>
> …you can see the atom-type assignments as labels, for example if the
> molecule was model 3:
> labelopt info idatmType
> label #3
> …and  can use the setattr command to change them, for example something
> like:
> setattr a idatmType N2  #3 at N8
> label #3
> I understand you may not know ahead of time about which atoms will have
> this problem, but this is the only way I can think of to directly control
> the protonation state of atoms in nonstandard residues with a command.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Aug 18, 2016, at 3:22 PM, Subha Kalyaanamoorthy <kalyaana at ualberta.ca>
> wrote:
> >
> > Hi There,
> >
> > Can anybody please suggest me how to use 'setattr' (or any other
> function) to assign a protonation state for an atom in a non-standard
> residue.
> >
> > I have a ligand and I am using a python script to add hydrogens and
> charge to the ligand molecule using chimera no-gui. I see that chimera adds
> an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of
> +1 to the molecule. Removing this hydrogen using GUI is simple but not
> practical for large set of molecules. So, it would be helpful if somebody
> suggest me a command-line to set specific protonation states for atoms (in
> non-standard residue).
> >
> > Thanks and Best Regards,
> > Subha
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users

Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160818/4b1298e9/attachment.html>

More information about the Chimera-users mailing list