Unfortunately, ViewDock, as one of the earliest chimera extensions, does not work in nogui mode. I've added this as bug #7799 in our bug database. The only workaround would be to run chimera with the DISPLAY environment variable set to a virtual X server, like Xvnc. Sorry about that, Greg On Fri, 16 Oct 2009, Aurelien Grosdidier wrote:

Dear all,

I'm trying to create a minimal chimera script that loads a PDB structure, then loads docking results (Dock format), saves the result and exits, as follows:

open mystructure.pdb viewdock myresult.dock4 "Dock 4, 5 or 6" save result.py stop

This works perfectly, when I launch Chimera (1.4rc 32-bits on Kubuntu 9.04 AMD64) :

chimera --script mkview.com

However, when I try to get rid of the display by adding the --nogui switch, chimera crashes with the following stack trace:

...Traceback (most recent call last): File "CHIMERA/share/chimeraInit.py", line 425, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1439, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 32, in func File "CHIMERA/share/Midas/midas_text.py", line 101, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 132, in _processFile File "CHIMERA/share/Midas/midas_text.py", line 64, in makeCommand File "CHIMERA/share/ViewDock/ChimeraExtension.py", line 42, in cmdViewdock File "CHIMERA/share/ViewDock/base.py", line 97, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 523, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 244, in __init__ File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI TclError: invalid command name "tix" Error while processing mkview.com: TclError: invalid command name "tix"

File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI

See reply log for Python traceback.

Any idea / workaround ?

Cheers,

-- Aurélien Grosdidier Molecular Modeling Group Swiss Institute of Bioinformatics

PS: I already tried Xvfb with no luck (segfault, this might be a *buntu bug, though).