[Chimera-users] command to show Structure Diagrams?

Eric Pettersen pett at cgl.ucsf.edu
Thu Feb 14 14:20:20 PST 2013

The Python would be:

from chimera import dialogs
from StructureDiagram.gui import StructureDiagramDialog
dlg = dialogs.display(StructureDiagramDialog.name)
dlg.updateImageFromSmiles("C1[C at H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2")

Put the above in a file with a ".py" suffix and just follow the instructions Elaine gave.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Feb 13, 2013, at 10:14 AM, Elaine Meng wrote:

> Hi Noel,
> Sorry, there is no command to show structure diagrams.  If the demo must do this, the only possibility (that I know of) is to do it in a python script.  In the demo, you can use the "open" command to open and execute the *.py file (the script, which would be one of your demo data files).
> For example, in the "Hormone-Receptor Complex Demo" that comes with Chimera, there is an "undo" command in panel 6 that opens a python script.  The script simply closes the sequence alignment window.
> I don't know python, so someone else would need to help with the script itself.
> 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 Feb 12, 2013, at 5:02 PM, Noel Pace wrote:
>> Dear Elaine, 
>> Thank you for your constant help...I am getting more proficient with the program language however I have encountered a difficulty and cannot resolve it using the manual.
>> I require the command to run the UTILITY: Structure diagram, then make it load SMILES code: C1[C at H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2
>> How can I make this possible please?
>> Thanks again,
>> Noel
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