Re: [PyMOL] How to ray trace clipped image without clipping spheres.

[Thomas H. <tho...@sc...>]

Along those lines: The script "SelectClipped" from the PyMOLWiki does a good job here, at least for spheres.

http://pymolwiki.org/index.php/SelectClipped

Example (after having loaded the script or installed it with the plugin manager):

PyMOL> select_clipped
PyMOL> hide everything, not clipped
PyMOL> clip atoms, 2, clipped

Cheers,
  Thomas

On Mar 11, 2013, at 4:38 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> # Hey :)
> 
> # Here is a work around...
> 
> # First import the numpy module
> import numpy
> 
> # Then store the viewing matrix as 6 by 3 numpy array.
> M=numpy.array(cmd.get_view()).reshape(6,3)
> 
> # Now place a pseudoatom at the position of the camera
> # Turn off autozoom to keep the view
> set auto_zoom, 0
> scale=1.0
> cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
> 
> # The dummy can now be used to hide all spheres within a cutoff distance. E.g.
> hide spheres, all within 150 of dummy
> 
> # You may need to play with the distance to get the right effect.
> # It is possible to use the distances of the original clipping planes,
> # by extracting those from the viewing matrix.
> # The 'scale' parameter can be used to adjust the effect.
> # If scale > 1, the dummy is placed behind the camera, which may be
> # required for a proper planar cut.
> # On the other hand, you can set it to < 1, to put the dummy closer to
> # the scene and cut out a spherical region.
> 
> # Note that you can change the view after this operation and have a
> nice sideview
> # of a clipped system, or use it to clip a system multiple times from
> different sides.
> 
> # Enjoy!
> 
> # Cheers,
> 
> # Tsjerk


-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor