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