From: Miguel <mi...@jm...> - 2004-12-26 03:35:36
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Mojca wrote: >> I saw in the povray doc that one of the primitive operations is moving= a >> sphere through space. One can define a spline/hermite curve for the >> sphere >> to follow. This is exactly what the 'trace' is. > > Below there's an example of its usage. I took an alpha helix, deleted > everything but the backbone atoms and traced through that atoms. Thank you. I will look at it. > - render/structures/backbone: > > There's currently only getAtomNumber() and getAtom...(int atomIndex) > defined in JmolViewer.java. This would need getCAlphaAtom...() function= s > or something similar. Yes, we need to build a series of functions that fetch data about the secondary structure shapes. > After that, one only has to draw a > sphere_sweep =7B linear_spline ... =7D through all the visible segments= , > longer than 1 residue. So, you are saying that a linear_spline simply travels from point to poin= t. Q: Currently the povray output generates cylinders for bonds. Within Jmol= itself it is a sphere_sweep. Do you think that export to povray should output cylinders or sphere_sweep for bonds? > - render/structures/trace: > > I didn't check how you determine the coordinates to draw it, but it > certainly needs > sphere_sweep =7B cubic_spline ... =7D through > I-don't-know-which-points-exactly. Trace passes through the midpoints between the alpha carbon atoms. These mid-points are used for several other secondary shapes too. > In any case, the user interface should give the user an option to > determine the radius of both the backbone and trace. The Jmol scripting language allows full control over the radius of backbone and trace. trace 0.5 OR trace 1.0 OR select all; trace .25; select helix; trace .5 Currently, the only way to access this functionality is by typing command= s into the scripting window. If people feel that more controls are necessary, then people should add controls to the Jmol application. The povray output should try to reproduce exactly what is on the Jmol scr= een. > For almost everything (atoms, bonds, backbone, trace, ...) I would also= > leave the user an option to choose if he wants to have the objects > transparent or not Transparency is something that Jmol currently cannot do. Perhaps that *should* be a povray option. > (like the option to choose the radius). again, the radius should be set within Jmol, then povray should output exactly what is displayed in Jmol. > This doesn't concern povray, but the java user interface: user can > easily show and hide the atoms and bonds. However, when displaying > structures, someone can turn them separately on, but then it's > impossible to turn perhaps only one or two of them off again. (Btw: > render/structures/off leaves the backbone display on.) All this functionality is available through the scripting language. If people do not want to use the scripting language to control these things then someone should build some gui controls ... that generate and execute scripts. >> The API through JmolViewer needs to be enhanced. Povray needs more >> information about the state of the display. In addition, there is >> currently no way to get any information for the secondary structure >> shapes >> (trace/ribbons/cartoons/....) > > It's certainly necessary to do something about that. JmolViewer seems t= o > be the the first step to be done towards enchancement of povray output.= Yes > Are my default settings wrong or is it generally so that povray > generates 26 (equal) images by default even though the picture is > static? I do not think I have every seen the povray code generate more than one file. But Nico has been working on it ... > I now manually add 'Final_Frame=3D1' into every .ini file. I do not know what this means. > Anyway: I have to thank a lot to all of you, people. You saved me a > whole bunch of time as I was short before implementing my own pdb2povra= y Glad that you like Jmol. We would like to have more of your help with povray output. I have not used povray very much, but I believe that it is a very important feature of the Jmol application. > and was looking for the most elegant way to display molecule vibrations= > animations (which would take me far too much time with much worse > results). Good. I will look at the povray output that you sent. Miguel |