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@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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