[Chimera-users] volume planes tool

Jeff Triffo triffo at rice.edu
Thu Aug 7 10:59:19 PDT 2008


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).


Elaine Meng wrote:
> Hi Jeff,
> That's definitely a Tom Goddard question, but he is away on vacation 
> this week.
> Pending a definitive answer, I am guessing it is not in the plans.  
> However, I believe you can do what you want by resampling the data on 
> a differently oriented grid, and then using the "Planes" feature on 
> that second, resampled set of data.  You would generate the resampled 
> data using the "Subregion selection" feature of Volume Viewer, by 
> turning on "Select subregions..." with the mouse, and after drawing 
> the selection box, turning on "Rotate selection box" and change the 
> orientation as desired, then clicking the Resample button.  This does 
> not mess up your original data, just creates an additional, resampled 
> data set.
> Downsides are that it may take some coordination or a couple of tries 
> to rotate the box as desired, and resampling causes some loss of 
> resolution.  It may be that resampling is necessary for showing 
> arbitrarily oriented planes, however, even if such an option were 
> added to the GUI.
> I hope this helps,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> On Aug 7, 2008, at 10:07 AM, Jeff Triffo wrote:
>> anyone know if the volume plane tool will support arbitrary orientation
>> of the plane any time soon?
>> -Jeff

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