[Chimera-users] Creating MultiScale surface from a script

Tom Goddard goddard at sonic.net
Tue Mar 24 15:56:53 PDT 2015

Hi Phil,

  The Multiscale tool won’t work in headless Chimera.  Unfortunately that code was written in antiquity and only operates through a GUI interface.  But you can use the Chimera “sym” command to get multiscale style surfaces of symmetric structures.  For example,

  open 2bbv
  sym #0 surf true

Check out the sym command documentation

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html>

I believe it works in the headless Chimera, although I have not tested that.


> On Mar 24, 2015, at 2:07 PM, Cruz, Phil (NIH/NIAID) [C] wrote:
> Hello Chimera users,
> I need to create a MultiScale surface from a Chimera python script when the model is of large structures such as virus particles.  On a Mac, the following lines work great:
> import MultiScale
> d = MultiScale.show_multiscale_model_dialog()
> d.make_multimers_cb(molecules=None)
> and produce the desired surface output.
> Unfortunately, where I really need this to work is on a Linux server using the special version of Chimera that doesn't require a graphics head.  When I run the script there I get errors, presumably when the script tries to create the dialog:
> Traceback (most recent call last):
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimeraInit.py", line 698, in init
>    midas_text.doRunScript("runscript", script)
>  File "/opt/UCSF/Chimera64-1.10.1/share/Midas/midas_text.py", line 2206, in doRunScript
>    execfile(scriptPath, scriptGlobals)
>  File "Chimera_Molecular.py", line 301, in <module>
>    d = MultiScale.show_multiscale_model_dialog()
>  File "/opt/UCSF/Chimera64-1.10.1/share/MultiScale/__init__.py", line 2296, in show_multiscale_model_dialog
>    return dialogs.display(MultiScale_Model_Dialog.name)
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 76, in display
>    dialog = find(name, create=1)
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 61, in find
>    return d()
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/baseDialog.py", line 665, in __init__
>    from tkgui import windowSystem
>  File "/opt/UCSF/Chimera64-1.10.1/share/chimera/tkgui.py", line 73, in <module>
>    import Togl
> ImportError: No module named Togl
> Is there a way to have the script create the multiscale surface without invoking the dialog (if that's what the issue is), or some other approach to get this to work in the required environment?
> Thanks for any suggestions.
> --
> Phillip Cruz, Ph.D.
> Contractor, Medical Science & Computing
> Computational Structural Biologist
> Computational Biology Section
> Bioinformatics and Computational Biosciences Branch (BCBB)
> 31 Center Dr., Room 3B62
> Bethesda, MD 20892-0485
> Office:  301-451-1089
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