[Chimera-users] Per-model clipping plane flickering

Tom Goddard goddard at cgl.ucsf.edu
Thu Feb 14 10:06:23 PST 2008

Hi Jeff,

  I think you need to increase the "cap to clip plane distance" in the 
Surface Capping dialog from its default value of 0.001 to maybe 0.01 or 0.1.

  I guess you have surface capping turned on.  Sometimes the clip plane 
partially clips the surface cap causing a fractured appearance of the 
cap.  The OpenGL clip plane is offset from the cap by a small amount to 
prevent this but the needed displacement depends on the precision of the 
OpenGL depth buffer.  Chimera should figure out the right value for this 
offset but currently it is specified by the user.


Jeff wrote:
> hi Tom,
> I am getting odd output using the per-model clipping plane - I have a 
> volume loaded w/ precomputed subsamplings, and have generated a 
> surface depiction of the volume. when I enable the per-model clipping 
> plane, there is a lot of blinking in the model at the interface with 
> the per-model clipping plane.
> this volume is a membrane that I masked out using contours (as I 
> explained a couple of emails ago, where I have a bunch of contours 
> plotted along a surface, and then use the zone tool along those 
> contours). this means that there are a lot of zeros where the masked 
> volume ends; could that be part of the problem?
> I am using Chimera build 2492, MacBookPro 2GB (identical model to 
> yours), and Leopard with the latest X11 patch.
> best,
> -Jeff

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