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

[Thomas Holder]

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  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


--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev
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Re: [PyMOL] How to ray trace clipped image without clipping spheres.

[Tsjerk Wassenaar]

# 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

--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev
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Re: [PyMOL] How to ray trace clipped image without clipping spheres.

[Jason Vertrees]

Hi Yarrow,

This is a known problem.
We'll try to fix this soon.

Cheers,

-- Jason


On Mon, Mar 11, 2013 at 2:05 PM, Yarrow Madrona  wrote:

> Hi,
>
> Does anyone know how to ray trace an image of an active site in sphere
> representation that is clipped, without getting a weird result that I
> assume comes from clipping the spheres? It looks like unfilled circles.
>
> Thank you
>
> -Yarrow
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>
>
> --
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
> http://p.sf.net/sfu/symantec-dev2dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev___
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[PyMOL] How to ray trace clipped image without clipping spheres.

[Yarrow Madrona]

Hi,

Does anyone know how to ray trace an image of an active site in sphere
representation that is clipped, without getting a weird result that I
assume comes from clipping the spheres? It looks like unfilled circles.

Thank you

-Yarrow


-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697




--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev
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