[Chimera-users] clip planes

Repic Matej matej.repic at epfl.ch
Fri May 8 12:35:47 PDT 2015

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.


Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne


From:  Bharat Lakhani <blakhani at wesleyan.edu>
Date:  Friday, May 8, 2015 at 17:45
To:  "chimera-users at cgl.ucsf.edu" <chimera-users at 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


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