[Chimera-users] volume planes tool

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 7 11:23:56 PDT 2008

Looking at Tom's "plans" page (http://www.cgl.ucsf.edu/chimera/plans.html 
), I see this feature listed there (#57).  According to the blurb for  
#57, Karin Gross and Christoph Best have written an extension called  
TomoPlane for doing this:  Christoph Best: TomoPlane


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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
> 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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