Hi Elain, Opening smiles in the command line using the syntax you pointed out works very nicely. Thanks a lot. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, March 01, 2012 7:04 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] reading SMILES description into Chimera Hi Boaz, You can just use the command line, for example: open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-] I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog. The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option. In that case you would just type or paste in the SMILES string in the indicated field. 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 Mar 1, 2012, at 7:08 AM, Boaz Shaanan wrote:

Hi,

I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what?

Thanks for your help.

Boaz

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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