[Chimera-users] drawing molecules

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 14 10:58:05 PDT 2008

Dear Kathleen,
There are some simple building capabilities, see Tools... Structure  
Editing... Build Structure:

Building from scratch is somewhat limited, in that it is more of a  
bond-by-bond accretion than sketching the molecule in quickly.  After  
building, you could use Minimize Structure (also under Tools...  
Structure Editing) to clean up the structure.

Instead of building from scratch, however, I'd recommend looking up a  
PubChem CID, if possible, or writing a SMILES string for your  
molecule.  These are options in the "Add Atoms" tab of Build  
Structure.  In those cases, the information is sent to a web server  
that sends back an already-minimized structure.

With the server approach, you may not get the protonation state you  
want, but you could simply delete any unwanted hydrogens and if  
necessary, use the AddH tool to add hydrogens.  AddH tries to generate  
protonation states reasonable near pH 7, whereas the server generally  
gives neutralized groups.

Structures in Chimera can be saved as Mol2 with File... Save Mol2.  If  
you want partial charges in the Mol2 output, you could use Add Charge  
before saving the file.

All the tools I mentioned are under Tools... Structure Editing in the  
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 11, 2008, at 2:49 AM, Kathleen.Zocher at ernaehrung.uni-giessen.de  

> Dear Sir or Madam,
> I`ve just one question concerning some special tools of Chimera. Is it
> possible to draw small molecules (ligands) within chimera? I can not
> find some information for this problem in the manual. For further
> docking experiments I just need a 3D-structure which is minimized (in
> a mol2 file).
> Many thanks in advance!
> Sincerely yours
> Kathleen Zocher

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