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

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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