There is a  workaround to this problem, which I used in a different program and have suggested in the past to Warren and others.  If getting the ray tracer to recognize the various clipping planes is difficult, this is probably the best solution.  It would be helpful, however, if Warren changed the POVray input files that are created by PyMOL a bit.  
    One can set up all the various parts of the picture, and then selectively show each element and clip it, with the others hidden.  Then output a POVray file.  This should only include the visible elements (correct, Warren?).  Hide this element, and show the next one, adjust the clipping plane, and output the POVray file.  One can then have a master POVray file which contains as many "include" statements as are needed to bring all the various elements together in one rendered image.  

  The difficulty in the current implementation of PyMOL is that the output for POVray contains both the scene definitions and the graphic primitives in one messy and potentially large file.  If the scene definitions could be stored in one small file, and the graphic primitives in another file, this process would be much easier.  One could then select one of the scene definitions files as the "master" and add "include" statements for all the graphic primitives as is needed.  I suppose this process is possible with the current POVray files, just not as simple.  I have examples if anybody is interested.


Sorry, still not done (I have made two attempts, but both failed).

While OpenGL supports arbitrary clipping planes, accomplishing this
correctly in the ray tracer is a much harder problem that one might


-----Original Message-----
From: Mankin Alexander []
Sent: Wednesday, April 29, 2009 6:18 AM
Subject: [PyMOL] object-specific Z-clipping

Dear all,
Does anyone know whether object-selective z-clipping has been
implemented in the newer Pymol version(s)? If not, has anyone found
any solution around (since 2002 no new threads on the matter)?
Shura Mankin

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