[Chimera-users] Using Chimera to read SMILES string into structure
miriam.gochin at tu.edu
Thu Sep 3 13:54:03 PDT 2009
You have solved my problem! If I use CONTROL-APPLE-v it works!!! (no middle mouse on a Mac).
Thank you so much.
I wonder if you could suggest how to fix this problem:
I am registered on chimera-users, because I have a profile and always get the chimera-users e-mails, but when I sent this request, it told me it would be held for the moderator (~ 24h) because I am not a member of the group. How do I become a member?
Touro University - CA
miriam.gochin at tu.edu
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 03, 2009 12:58 PM
To: Miriam Gochin
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Using Chimera to read SMILES string into structure
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
> 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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