[Chimera-users] Axis vs map rotation

Tom Goddard goddard at sonic.net
Thu Dec 8 16:17:49 PST 2011

Hi Nicolas,

   There is not a command to shift or position an oblique volume slice.  
I agree that would be useful and will put a feature request in our 
database for it.

   Here's a way to do what you want.  Use the subregion selection green 
outline to crop to a rotated box.  Make the box have a thickness that 
covers your structure of interest.  This creates a new volume shown in 
the volume dialog and you can use the Planes panel to flip through 
planes of that rotated volume separated by precisely the grid spacing.  
The grid spacing can be specified using the entry field at the end of 
the "Rotate selection box" line in the subregion panel.  It defaults to 
match the original data set grid spacing.   To control the width and 
height of the rotated volume you can use the Region Bounds panel of the 
volume dialog to specify exactly how many voxels to use along each axis 
for display of the rotated volume.


-------- Original Message --------
Subject: Re: [Chimera-users] Axis vs map rotation
From: Nicolas Coudray
To: Tom Goddard
Date: 12/8/11 6:08 AM
> Hello Tom,
> Thanks for the answer...
> It is a nice alternative. Although, it's kind of more difficult to 
> manually translate a precise amount of nm. Is there a way, like with 
> the "plane" option, to control precisely the width and the translation 
> of the subregion box? Maybe through a command line, but I have found 
> it...
> Thanks again for the help,
> Nicolas
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>     ------------------------------------------------------------------------
>     *From:* Tom Goddard
>     *To:* Nicolas Coudray
>     *Cc:* chimera-users at cgl.ucsf.edu
>     *Sent:* Wed, 07 Dec 2011 19:00:01 -0500
>     *Subject:* Re: [Chimera-users] Axis vs map rotation
>     Hi Nicolas,
>       To show an oblique slice of a map you can use the volume dialog
>     "subregion selection" panel.  The "planes" panel can only display
>     slices perpendicular to the volume axes as you found.  There's a
>     video showing how to show the oblique slice on the Chimera video
>     tutorial web page
>     http://www.cgl.ucsf.edu/chimera/videodoc/slice/index.html
>     The Chimera volume guide has a text description of the procedure.
>     http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#resample
>       Tom
>>     Hi,
>>     I'm using the "Feature >> Plane" options of the "Volume viewer
>>     tool" to show contour lines in planes of density maps. For the
>>     plane, there are 3 options: "X-axis", "Y-axis", and "Z-axis". The
>>     plane I'm interested in is none of those. I try to rotate the
>>     maps, but the X, Y and Z axis are also rotating... Do you know if
>>     there's a way to rotate the "axis" and the "map" independently,
>>     please?
>>     Thanks in advance,
>>     Nicolas

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