How do I measure angles and distances in pymol???
Michael Ford pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ad...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > Today's Topics: > > 1. Question on clipping with surfaces (Timothy Moore) > 2. Re: Question on clipping with surfaces (Warren L. DeLano 1) > > --__--__-- > > Message: 1 > Date: Wed, 04 Sep 2002 14:56:42 +0100 > From: "Timothy Moore" <mrx...@nottingham.ac.uk> > To: <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] Question on clipping with surfaces > > Hello all, > > I don't know whether this has been covered before but I have some > questions on clipping whilst using surfaces. Before I go on I will state > that pymol produces the best surfaces for my purposes, of any program I > have seen so far. However, (sorry there is always room to be better! ;) > ) the ideal situation would be if the cut "surface" was represented as > if the molecule was solid. ie: you didn't see inside the molecule > itself, but the cut plane. Is there any way to do this (e.g. via povray > rendering)? I appreciate it is probably not exactly easy though. > > Alternatively, it would be good if it was possible to make the inside > surface of a molecule appear completely black without resorting to > ambient=0. > > Any ideas? > > Tim > > --__--__-- > > Message: 2 > Date: Wed, 4 Sep 2002 07:45:09 -0700 (PDT) > From: "Warren L. DeLano 1" <war...@sunesis.com> > To: Timothy Moore <mrx...@nottingham.ac.uk> > cc: <pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] Question on clipping with surfaces > > On Wed, 4 Sep 2002, Timothy Moore wrote: > > > I don't know whether this has been covered before but I have some > > questions on clipping whilst using surfaces. Before I go on I will state > > that pymol produces the best surfaces for my purposes, of any program I > > have seen so far. However, (sorry there is always room to be better! ;) > > ) the ideal situation would be if the cut "surface" was represented as > > if the molecule was solid. ie: you didn't see inside the molecule > > itself, but the cut plane. Is there any way to do this (e.g. via povray > > rendering)? I appreciate it is probably not exactly easy though. > > > > Alternatively, it would be good if it was possible to make the inside > > surface of a molecule appear completely black without resorting to > > ambient=0. > > Tim, > > What you're asking for is mathematically non-trivial. In fact, I > haven't even solved this problem for spheres yet in the raytracer. > > As far as I can tell, setting ambient to zero alone doesn't quite do > the job, since some triangles still get lit by the light source. > > The best combination I can find is: > > set ambient=0 > set direct=0.7 > set reflect=0.0 > set backface_cull=0 > > While gives no shadows an only a few artifacts. > > As an alternative, you might just consider showing the inside of the > surface directly...that will create less visual artifacts, and so long as > ambient and direct are sufficiently low, it will look reasonable in "ray". > > util.ray_shadows("heavy") > set two_sided_lighting=1 > set backface_cull=0 > > Cheers, > Warren > > --__--__-- > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > End of PyMOL-users Digest
