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

Miriam Gochin miriam.gochin at tu.edu
Thu Sep 3 11:16:51 PDT 2009

Hi Elaine,

I can see that the problem is that I can't copy and paste anything at all, eg. I can't copy a command from a file using command-c and paste it using command-v on the Chimera command line.  It gives an error (a sound).  But I can copy and paste into text files etc.  I'm using Mac-OSX-10.4.11 on a PowerPC.

Miriam Gochin
Touro University - CA
miriam.gochin at tu.edu
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 03, 2009 10:46 AM
To: Miriam Gochin
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Using Chimera to read SMILES string into structure

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-

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 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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