If clipping isn't the effect you want, the solution probably lies in increasing the camera field of view angle which will enable PyMOL to better "get of inside" spaces without having nearby elements appear to intersect the camera surface (or front clipping plane).
set field_of_view, 45
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From: QT [mailto:rdirective@gmail.com]
Sent: Monday, November 10, 2008 12:15 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Camera Orientation

Hello everyone,

I have a question regarding camera orientation.  I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded.  Clipping plane is not useful because I don't want the surface to disappear.  In a sense, I want to change the default camera orientation of pymol from "looking in" to "looking out".  This is much like standing in a room and looking around.  I think the answer lies in the 18 parameters of set_view, but which should I change and how are these computed?

Quyen Tran

Department of Biochemistry
University of Houston