[Chimera-users] reading SMILES description into Chimera
bshaanan at exchange.bgu.ac.il
Thu Mar 1 09:17:29 PST 2012
Opening smiles in the command line using the syntax you pointed out works very nicely.
Thanks a lot.
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
E-mail: bshaanan at 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 at cgl.ucsf.edu]
Sent: Thursday, March 01, 2012 7:04 PM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] reading SMILES description into Chimera
You can just use the command line, for example:
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 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:
> 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 Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> E-mail: bshaanan at bgu.ac.il
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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