[Chimera-users] yet another chimera question...

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 19 11:00:43 PST 2007

Hi Jeff,
There isn't a command (unless Tom Goddard has made an accelerator for 
this), but if I were trying to position the per-model clipping plane 
normal to a volume data axis I would take this approach:

(1) align volume data using the Orient button on Volume Viewer.  This 
will point the axes of the current data set in the standard directions: 
X horizontal in the plane of the screen increasing rightward, Y 
vertical in the plane of the screen increasing upward, and Z 
perpendicular to the screen increasing outward from the screen.
(2) depending on which axis you want the per-model clipping plane to be 
normal to, optionally use the command "turn" to rotate the volume data 
90 degrees around some axis
(3) use the "Orient plane" button on Per-Model Clipping to place the 
plane perpendicular to the line of sight, and optionally the "Flip 
plane" button depending on which side you want to be visible

For example, to align the per-model clipping plane normal to the Z axis 
of the data, you could skip #2 above.  To align the per-model clipping 
plane normal to the X axis of the data, step #2 would be to use the 
command "turn y 90" or turn y -90" (aligning the data X axis along the 
laboratory Z axis).  A little bit of a brain teaser...

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 16, 2007, at 2:05 PM, Jeff wrote:

> thanks Tom,
> is there a command to set the per-model clipping plane to intersect an
> axis (like the x, y, or z axis of a volume map, or the global x, y, or 
> z
> axis, etc)
> -j
> Thomas Goddard wrote:
>> Hi Jeff,
>>   The Chimera "savepos <name>" command allows you to save views 
>> including
>> clip plane positions.  You return to a view with command "reset 
>> <name>".
>> The named views are saved in Chimera sessions.  So you can just keep
>> one Chimera session with as many named views as you want.  The "reset 
>> list"
>> command lists all named views.
>> 	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html
>>    Tom
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