Using Chimera to read SMILES string into structure
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.
Miriam Gochin Touro University - CA miriam.gochin@tu.edu 707-638-5463
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.
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@tu.edu 707-638-5463 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 03, 2009 10:46 AM To: Miriam Gochin Cc: chimera-users@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.
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
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?). Elaine
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@tu.edu 707-638-5463 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 03, 2009 10:46 AM To: Miriam Gochin Cc: chimera-users@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.
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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?
Miriam Gochin Touro University - CA miriam.gochin@tu.edu 707-638-5463 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 03, 2009 12:58 PM To: Miriam Gochin Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Using Chimera to read SMILES string into structure
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?). Elaine
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@tu.edu 707-638-5463 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 03, 2009 10:46 AM To: Miriam Gochin Cc: chimera-users@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.
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Hi Miriam, Glad you can paste now!
Now for the other problem... My guess is that the email address that your sent messages are marked with is slightly different than the one given when you first signed up for chimera-users. For example, the messages you sent could be marked as sent by name@school.edu whereas the initial signup could have been something like name@machine.school.edu, or vice versa. In that case, messages sent to either would still reach you, but on one address would be recognized as already belonging to the chimera-users list.
That is only a guess, however. If I'm right, the way to fix it would be to either
(a) unsubscribe the existing subscription and sign up again with address that matches your outgoing signatures (these can be done at <http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
)
(b) change your mail setup so that your sent mail is marked with the other version of your email address
Perhaps others who know more about this (Conrad?) can pipe up if my guess and/or suggestions are wrong... 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 3, 2009, at 1:54 PM, Miriam Gochin wrote:
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?
Miriam Gochin Touro University - CA miriam.gochin@tu.edu 707-638-5463
Hi Elaine
I'm using the <open smiles> command as per your instructions (see your message below).
The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
What I get is nonanol. The program returns
opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
Obviously, I'm using a different SMILES convention than Chimera.
I'd appreciate you suggestion regarding the SMILES convention, I should be using.
All the best
George
George T. Tzotzos, PhD Dept. of Molecular Genetics Univ. of Gent, Belgium
On Sep 3, 2009, at 7:46 PM, Elaine Meng wrote:
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.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi George, The smiles->3D conversion is done by a Web service at Indiana University, and as far as I know it uses the standard SMILES notation as described by Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
However, I did reproduce the problem you reported, which seems to be related to the slashes (\ /) in the string. For example, you do get the correct molecule, albeit without control over stereochemistry, with smiles:CC=CC=CCCCCCCCCCO
The status line message suggests that Chimera may be processing the string incorrectly before sending it to the Web service, but we will have to investigate that further and get back to you. I'll file a bug report and put you on the notification list (you will get some additional messages about that later). If it is a limitation of the Web server, however, we may not be able to fix it. In the future, if you run into another problem that could be a bug, please use "Help... Report a Bug" in the Chimera menu to send us the information -- that will automatically include what version of Chimera and type of computer you are using, since sometimes those are important. Best, 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 27, 2009, at 10:40 AM, George Tzotzos wrote:
Hi Elaine
I'm using the <open smiles> command as per your instructions (see your message below).
The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
What I get is nonanol. The program returns
opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
Obviously, I'm using a different SMILES convention than Chimera.
I'd appreciate you suggestion regarding the SMILES convention, I should be using.
All the best
George
George T. Tzotzos, PhD Dept. of Molecular Genetics Univ. of Gent, Belgium
On Sep 28, 2009, at 8:55 AM, Elaine Meng wrote:
Hi George, The smiles->3D conversion is done by a Web service at Indiana University, and as far as I know it uses the standard SMILES notation as described by Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
It turns out that the web service at Indiana University wasn't handling SMILES with forward slashes correctly, only translating the string after the last slash. They have fixed that bug and Chimera will now get the right structure for your SMILES string.
--Eric
However, I did reproduce the problem you reported, which seems to be related to the slashes (\ /) in the string. For example, you do get the correct molecule, albeit without control over stereochemistry, with smiles:CC=CC=CCCCCCCCCCO
The status line message suggests that Chimera may be processing the string incorrectly before sending it to the Web service, but we will have to investigate that further and get back to you. I'll file a bug report and put you on the notification list (you will get some additional messages about that later). If it is a limitation of the Web server, however, we may not be able to fix it. In the future, if you run into another problem that could be a bug, please use "Help... Report a Bug" in the Chimera menu to send us the information -- that will automatically include what version of Chimera and type of computer you are using, since sometimes those are important. Best, 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 27, 2009, at 10:40 AM, George Tzotzos wrote:
Hi Elaine
I'm using the <open smiles> command as per your instructions (see your message below).
The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
What I get is nonanol. The program returns
opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
Obviously, I'm using a different SMILES convention than Chimera.
I'd appreciate you suggestion regarding the SMILES convention, I should be using.
All the best
George
George T. Tzotzos, PhD Dept. of Molecular Genetics Univ. of Gent, Belgium
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Eric Pettersen -
George Tzotzos -
Miriam Gochin