[Chimera-users] about transformation matrix

[Tom Goddard]

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
>
>
>
> Hi Julio,
>
>     The details of the fitting algorithm are given in the User's Guide.
>
>
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html
>
> You should definitely read that if you want the best understanding.  But
> the brief answers to your questions are that the convergence criteria
> looks for optimization steps of less than 0.01 grid index to decide
> convergence.  The user interface does not allow you to change the 0.01
> grid index criteria -- it could be done by editing a line of Python.
> The default settings do mask using the contour level of the fit map as
> an outer boundary.  So that level is important.
>
>       Tom
>
>
>