[Chimera-users] failure to add-H to quaternary C

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 5 09:46:35 PDT 2017


HI Francesco,
It is probably that the automatic atom-type identification does not assign the type that you wanted, maybe because it is difficult to tell from the atomic coordinates.  Atom types are listed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

The workaround is simply to change the atom type to sp3 carbon right before adding hydrogens.  In your case, in the model from the pdbqt file, select just the carbon whose type you want to change (Ctrl-click) and then use command

setattr a idatmType C3 sel

Or, instead of “sel” to specify the selected atom(s), you can specify by name, for example if it was atom C12 in residue DTP:

setattr a idatmType C3 :DTP at C12

You can label to show atom type.  Example commands to label the selected atoms:

labelopt info idatmType
label sel

The labels will not change automatically, so if you showed these labels before changing the type, you have to show labels again (using command or menu) to show the new type.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 5, 2017, at 12:15 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> pdbqt from autodock-vina -> pdb with chimera -> addH with chimera.
> 
> Chimera fails (systematically) to add one H to a quaternary carbon of the diterpenoid.
> 
> avogadro (which does not understand pdbqt) does the addH job correctly from chimera-savedpdb.
> 
> Should Eric be interested, I could send (privately) the file
> 
> best regards
> 
> francesco pietra




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