Hi Bharat, To be able to properly slice the protein in half you should first orient it along a principal axis. One way you can achieve this is as follows: 1. Define an axis for the whole protein You can use Tools > Structure Analysis > Axes/Planes/Centroids or via command line define axis #0 (assuming you want to work on model #0; the new axis should have the name a1) 2. Align the view with the axis (command line) align a1 If necessary orient like this (command line) turn x 90 (turn y 90 or whatever axis and angle suits your purpose) 3) Make a surface representation of the protein surf #0 4) Use Per-Model clipping to position the clipping plane. Adjust surface capping as desired. At any rate, the rendering will not be ideal, since for proper (and much nicer) depth depiction of surfaces one should use ambient occlusion lightning, which is not available afaik, unless you put a lot of effort into manually setting up a POV-Ray job for this. Best, ------------------------------------------------------ Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: Bharat Lakhani <blakhani@wesleyan.edu> Date: Friday, May 8, 2015 at 17:45 To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] clip planes Dear All I want to visualize the core of my protein, Is it possible to slice the protein right into two half in order to visualize the core of the protein. I tried using chimera pre-capping model but it has not been work out well. Any suggestion on this would be great. Thanks