Re: [PyMOL] How to ray trace clipped image without clipping spheres.
Hi Yarrow, This is a known problemhttp://sourceforge.net/p/pymol/feature-requests/53/. We'll try to fix this soon. Cheers, -- Jason On Mon, Mar 11, 2013 at 2:05 PM, Yarrow Madrona amadr...@uci.edu 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___ 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
Re: [PyMOL] How to ray trace clipped image without clipping spheres.
# 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 ___ 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
Re: [PyMOL] How to ray trace clipped image without clipping spheres.
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 tsje...@gmail.com 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 ___ 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