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

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 3 12:58:13 PDT 2009

Hi Miriam,
Are you using X11 Chimera or Aqua Chimera?  In the X11 one I had to  
click middle mouse button instead of using command-v.  Maybe it would  
be better if you used "Help... Report a Bug" instead of sending mail  
to chimera-users, since that bug dialog automatically includes  
information on which Chimera you are using and your system.  We  
probably can't offer advice unless we can reproduce the problem.

You would need to describe the problem again and include your e-mail  
address on the report.  Also explain what you mean by "I can copy and  
paste into text files" (how did you do it? menu? command-c and command- 
v?  are you using Word, Text-edit, or Terminal?).

On Sep 3, 2009, at 11:16 AM, Miriam Gochin wrote:

> 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
> 707-638-5463
> ________________________________________
> 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-
> 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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