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:
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
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 - the box, but cannot paste it in, which I need to do. Thanks for your help.
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