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: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ images.html#matching 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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu