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

George Tzotzos gtzotzos at mac.com
Sun Sep 27 10:40:38 PDT 2009

Hi Elaine

I'm using the <open smiles> command as per your instructions (see your  
message below).

The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- 
ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO

What I get is nonanol. The program returns

opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues

Obviously, I'm using a different SMILES convention than Chimera.

I'd appreciate you suggestion regarding the SMILES convention, I  
should be using.

All the best


George T. Tzotzos, PhD
Dept. of Molecular Genetics
Univ. of Gent, Belgium

On Sep 3, 2009, at 7:46 PM, Elaine Meng wrote:

> 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-
> dependent.
> 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 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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