Hi Julio

The Chimera fitting code does a full 3-degree-of-freedom rotational search.  It cannot search fewer rotational degrees of freedom.  It would be nice to adapt the code to be able to consider only rotations about an axis.  The needed changes would be in the FitMap Chimera module not the fitnogui.py script.  Optimizing using only two rotational degrees of freedom that are Euler angles seems like a bizarre case and we are not likely to ever handle that.

Please post future questions to the chimera-users mailing list so others can answer and read the answers.

    Tom

Hi Tom,

Sorry to bother you again.  Is there a way fix one of the Euler angles for the fitting?  Since we have a small theta, we would like to fix psi=0, and optimize on phi and theta only, plus the translations.  I'm using the fitnogui script.

Many thanks,
Julio


On Jul 28, 2010, at 5:13 PM, Tom Goddard wrote:


Hi Julio,

  I guess you are using the fitnogui.py script.


http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py

The parameters are right near the top -- ijk_step_size_min is the one
you're interested in.

  The initial contour level is set as described in the documentation:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf

  The "volume" command can set the contour level:

    volume #0 level 27.6

 Tom

Hi Tom,

Thanks again. Editing the line of code would be perfect for us, since we are calling Chimera from our program with the "nogui" option. Could you point me the place where I need to change that 0.01?

What happens with the contour level when I'm calling Chimera in that way (nogui)?  Can I similarly set it somewhere in the code? Or with an option in the command line?

Best,
Julio