[PyMOL] clipping planes
Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks fine. Best Regards Christian -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] clipping planes
Christian, you should be able to get the values from the tuple returned by get_view(). Looking into this would be a good starting point. from my old notes (origin unknown...): 0-8 is the 3x3 rotation matrix 9-11 is the camera location (I think -- been a while...) 12-14 is the origin of rotation 15-16 are the clipping distances and 17 is the orthoscopic flag. Cheers, Carsten -Original Message- From: Christian Roth [mailto:christian.r...@bbz.uni-leipzig.de] Sent: Friday, June 15, 2012 12:57 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] clipping planes Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks fine. Best Regards Christian -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
[PyMOL] Clipping planes and slab thickness for different objects?
I have one object showing the surface of a protein and another object showing a ligand inside the protein. Is it possible to use the clip command to define different clipping planes for the 2 objects. I want so cut the proteinsurface using clip, but the Ligand inside the protein should not be clipped, but displayed completely. Thanks, Stephan Tatzel
Re: [PyMOL] Clipping planes and slab thickness for different objects?
I have one object showing the surface of a protein and another object showing a ligand inside the protein. Is it possible to use the clip command to define different clipping planes for the 2 objects. I want so cut the proteinsurface using clip, but the Ligand inside the protein should not be clipped, but displayed completely. I assume that PyMOL's clipping planes are simply OpenGL clipping planes, in which case the answer is no. They're handled in hardware, not by the application. -Nat
[PyMOL] clipping planes
I don't understand how these work at all. Is there any straightforward way, given a structure's position and dimensions and the desired camera position, to calculate the ideal position for the plane? How does PyMOL decide where to put the planes? Right now I'm missing by a small amount and atoms disappear randomly. thanks, Nat
