[Chimera-users] Adding Hydrogens to Dexomethasone Misses 1 Atom

BATUHAN KAV bkav13 at ku.edu.tr
Wed Aug 27 00:36:29 PDT 2014

Dear Elaine,

Thank you for your suggestion. It solved my problem. I am quite new to
Chimera and I missed this very trivial part. Thank you again.


On Tue, Aug 26, 2014 at 8:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Batuhan Kav,
> It is because the geometry (bond lengths and angles) are different in the
> two molecules.  Chimera uses these to try to figure out the atom types.  In
> the "correct" molecule, C6 is identified as atom type C3 (sp3-hybridized
> carbon), whereas in the "incorrect" molecule, it is identified as atom type
> C2 (sp2).
> You can manually assign C6 to the correct atom type before adding
> hydrogens, for example with command:
> setattr a idatmType C3 @C6
> You can see the atom types by labeling, for example menu "Actions… Label…
> IDATM Type" to label the currently selected atoms.   You would have to
> re-label (choose this menu item again) after changing the type to see the
> change.
> 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 26, 2014, at 6:45 AM, BATUHAN KAV <bkav13 at ku.edu.tr> wrote:
> > Dear All,
> >
> > I am trying to add hydrogen atoms to dexomethasone ligand. In the
> original PDB file, there are two dexomethasone molecules. So, I create
> split them into two different PDB's. Then, I load them and use addH option.
> In one PDB (sil.pdb), everything works fine and all hydrogens are added
> successfully. However, in the other pdb (which I name as other.pdb), one
> hydrogen atom is missing. I will use these files for further
> parametrization in AMBER, so this is really important. I looked through the
> files over and over again but couldn't find any reason for this apparent
> difference. What am I missing? I also attach the files. Any help would be
> greatly appreciated.
> >
> > Cheers
> > <sil.pdb><sil-2.pdb><other2.pdb><other.pdb>
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