[Chimera-users] about transformation matrix

[Julio]

Hi Tom,

Excellent!  I will try adjusting those parameters.

Thanks very much.
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
>>
>>
>>
>> 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
>>
>>
>>
>