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

Dear Bharat, Maybe you were using global clipping (such as in the Side View) and showing a cap. There is another clipping tool that allows clipping at different angles, and only clipping certain models. Take a look at Per-Model Clipping (in menu under Tools… Depiction). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mode...> Here’s another example image of a per-model-clipped surface: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/kchan/kchan.html> If you really wanted to cut the protein with a flat plane and then show both sides, you would need to: (1) open the structure (2) enable per-model clipping on that structure (or show surface, then enable per-model clipping on that surface) (2a) adjust clipping with mouse, then do other things (coloring etc.) as desired for the image (3) save image (4) flip plane 180 degrees (there is a button for this in the dialog) (5) rotate structure so you can see the cut side (could use command “turn x 180” to rotate 180 degrees, more precise than trying to do it with the mouse) (4) save another image The two images could be separate panels or you could use some standard image-edting program to combine them into a single image file. In the case of non-planar splitting (for example, showing the interface between protein chains), see the “opened interface image tutorial” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On May 8, 2015, at 8:45 AM, Bharat Lakhani <blakhani@wesleyan.edu> wrote:

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