From: "Miguel" <[EMAIL PROTECTED]> > Nico wrote: > > > Concerning the output of secondary structure : the output of the 'Trace' > > structure seems to work > > Unfortunately, I am unable to get this to work properly. > > If I change showPolymers to true then I get warnings about the camera and > fog. Then the rendering process proceeds very slowly. And the end result > is speckled with blue pixels.
What I see on my side : - no warning - rendering process is a lot slower (about 5 times slower, but depending a lot on the molecule). I think it is normal, splines are a lot more complex than spheres and cylinders and they are also a lot bigger. - no problem with the end results : do you use the .ini file to render ? if you use the .pov file directly there is no antialiasing by default. If you're editing the .pov file directly from povray you have to switch to the .ini file before clicking Run. Maybe you can send me the .ini and .pov files that are causing problems ? I can check here if I have the same problems. > I observe that your spline is colored blue, so I assume that is where they > are coming from. Probably. I saw those speckles once but I was rendering with mosaic preview turned on. They disappeared on the last pass of the rendering. > > but there is still work to do on it : > > - add method on Viewer to get the radius of the spline > > Yes. > > Note that the radius of the spline can vary along the length of the trace.. Ok, radius can be specified for each control point, but I have to look at povray doc to see what it means for bspline (I define n+2 control points when there is n points to go through). Maybe to work also with the color part (see below) > > - add method on Viewer to get the color of the spline > > The color can also change along the length of the trace. > > This tells me that the spline should be output in segments, where each > segment gets its own color and radius. It is possible by creating n-1 spline with 4 control points instead of 1 with n+2 control points : spline 1 uses control points 1, 2, 3, 4 spline 2 uses control points 2, 3, 4, 5 ... spline n-1 uses control points n-1, n, n+1, n+2 > > - add method on Viewer to tell if traces (globally) or trace > > (individually) should be displayed > > Within Jmol this is handled by checking the radius of the trace. If the > radius is 0 then there is no trace for that segment. Ok > > I think the 'Trace' structure is a good example of what the PovraySaver > > needs to output correctly the structure. We should do it clean before > > moving to other structures. > > Yes. > > The other simple one is 'backbone'. It behaves almost exactly like > 'trace', except the representation is cylinders that run directly from one > alpha carbon to the next. What internal data stores the information for backbone ? > > IMHO, before going on the povray output, we should really work on what the > > viewer should provide access to and how it should be done. > > I'm not sure I can help on this part, so I will wait for the moment. > > OK. > > I think that we need to try to come up with an API that allows us to pass > in a string as a symbolic name for the shape we are interested in. By that > mechanism we can avoid creating an entry point for each shape. It may be a solution. Adding an entry point for each shape, and each property of each shape would not be very handy. Nicolas ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
