[Chimera-users] Fitting with constrained motion

[Tom Goddard]

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
>>>
>>>
>>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100806/ef5a6195/attachment.html>