[Chimera-users] Using Chimera to read SMILES string into structure

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 3 10:46:25 PDT 2009

Hi Miriam,
Are you on a Mac?  I'm using a Mac and was able to copy text from  
Terminal and paste it into both those places.  The copy/paste  
procedure depends on your platform.  Using the Mac aqua version, I  
highlighted text in Terminal and pressed command-c to copy, then to  
paste, I clicked into the blank dialog text area and pressed command- 
v.  Using the Mac X11 version, I used the same copying procedure but  
then to paste, clicked into the blank dialog text area and then  
clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c  
and Ctrl-v.

You can also get SMILES->3D from the Chimera command line, e.g.

open smiles:C1CCC(O)CC1

and the copy/paste procedure there is the same, but again platform- 

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:

> I have downloaded the latest build (Aug 30, 2009) and don't seem to  
> be able to input a SMILES string.  I have tried both the Utilities - 
> > Structure Diagram and the Structure Editing -> Build Structure  
> tool, and in both cases I can see a box to input the SMILES string,  
> but the copy and paste mechanism won't work.  I can enter text in  
> the box, but cannot paste it in, which I need to do.  Thanks for  
> your help.

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