[Chimera-users] clipping related models identically

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 6 13:27:37 PST 2008

Raven Huang asks (paraphrased):

> I have four related structures that I want to show in cutaway view,  
> with the cut being in the same place in all the structures.  How  
> can I do that?

	The technique varies depending on whether you are clipping using the  
global clip planes (i.e. the ones shown in the Side View), or with  
per-model clip planes (from the Per-Model Clipping tool).  Both  
techniques share the same setup step though:  open all your models  
and get the parts you care about superimposed.  If the starting  
coordinates are already "in the same reference frame" then you don't  
have to do anything but open the models.  Otherwise you will have to  
superimpose them either with the MatchMaker tool or the "match"  
command.  There is a discussion of using those here:


	To view just one of the structures at a time, use the Model Panel  
(Favorites->Model Panel) and use the buttons in the Shown column (or  
the Show Only button in the button list) to show one structure/ 
surface.  Now for adjusting the clip plane...

Global clipping:  open the Side View and adjust the near clip plane  
until it is cutting where you want it to.

Per-model clipping:  use the Per-Model Clipping tool to adjust the  
clip plane of the visible model until it is cutting where you want it  
to.  Then choose one of the other models you want to cut from Per- 
Model Clipping's "Model:" menu.  Enable clipping and click the "Align  
plane" button once you have chosen the original model in the menu  
next to the button.   The model clip planes will now be aligned.

	Once the models are all clipped, you can either show then  
individually (the Model Panel again) and save separate images, or  
move them apart using the "move" command and save one combined image.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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