Yup, thanks for your help that did it.  Although the script didn't spring back to the default camera anchor point after it did the 360 degree rotation about y-axis, I understand now.  So, to move the camera anchor point around, you modify the parameter 9-11 of set_view(), which controls the x,y,z anchor point of the camera.

Now I've come to understand that parameter 15 and 16 essentially define the clipping plane.  How are these related to each other because I also want to do sectioning of the ribosome tunnel from front to back in 10A increment.

Is the clipping plane static or can you also rotate the clipping plane to do horizontal and diagonal sectioning, or is that accomplished by rotating the structure about its axis?

By default the clipping plane sections from front to back or vertical sections.


On Tue, Nov 11, 2008 at 12:30 AM, DeLano Scientific <delsci@delsci.info> wrote:
Ah ha, now I see what you're angling at!  What a great question -- I'm
amazed this hasn't come up before in ten years of usage and development.

The core problem is that PyMOL's camera has been designed from day one to
orbit around a specific point in space, not at a point.  To get the effect
you desire, I think you'll need to transiently back up the camera, rotate it
about its prior orgin and then move it back again.  Here's an example script
which does that:

load $TUT/1hpv.pdb
set field_of_view, 45
zoom organic
orient organic
show stick, polymer
show surface
set surface_color, white
set transparency, 0.5
clip slab, 30
set line_width, 5



def spin():
   from pymol import cmd
   for x in range(360):


python end



From: QT [mailto:rdirective@gmail.com]
Sent: Monday, November 10, 2008 10:04 PM
To: DeLano Scientific
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Camera Orientation

Ah thank you Warren, that gave it a fish-eye effect that seems to work.  Is
there any other way to go about this problem?  Is there no way to move the
camera from looking in to looking out?  By default, the camera is anchored
outside the molecule, can the camera be anchored to a point inside the
molecule but not on any atom?


On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <delsci@delsci.info>


       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

       DeLano Scientific LLC
       Subscriber Support Services


       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

       Quyen Tran

       Department of Biochemistry
       University of Houston