[Chimera-users] volume planes tool

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 7 11:19:19 PDT 2008

Hi Jeff,
Tom may add this to his requests list when he returns, but I can't  
make promises on his behalf!  As you can see, the list is pretty  
long:  http://www.cgl.ucsf.edu/chimera/plans.html
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 7, 2008, at 10:59 AM, Jeff Triffo wrote:

> yes,
> that would work but seems tedious for frequent use, and assumes the  
> desired orientation is known. There is a capability in IMOD to do  
> this "live" through their 3dmod Slicer viewer - which I have been  
> assuming just does on-the-fly interpolation of the data, because it  
> is a live update. It's an incredibly useful function to have access  
> to because the user is often "hunting" for the right orientation for  
> a slice, and I often find myself wanting it in Chimera. So I find  
> myself doing quite a bit of pre-work modeling in 3dmod prior to  
> being able to jump to Chimera.
> but, for now, I could just find desired orientations in IMOD, and  
> try to reproduce that using a resampling of the entire volume in  
> Chimera. In my case, that would require knowing the relationships  
> between the Euler convention in 3dmod and Chimera, along with where  
> each program defines the center of rotation (which I have looked  
> into many times for various reasons - such as using IMOD models  
> superimposed with volume displays in Chimera - but always forget  
> soon after).
> -Jeff

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