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. Tom
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) OCICB/OSMO/OD/NIAID/NIH
31 Center Dr., Room 3B62 Bethesda, MD 20892-0485 Office: 301-451-1089 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)
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