From: Miguel <mi...@jm...> - 2005-01-20 17:05:45
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Gunnar wrote: > I have downloaded the source code for Jmol, and currently am in the > process of looking through how you render all the elements, as well as = the > importing and exporting features of Jmol. I am very interested in being= > able to work on this project to further enhance the capabilities of Jmo= l. Good. > However, I would like to understand more about the project first. If yo= u > don't mind, I have a few questions for you. > > 1) I have seen that you clip the diameter of spheres in the Sphere3D.ja= va, > part of the g3d package to 128 maximum using the maxSphereCache variabl= e. > What unit does the 128 refer to? Is it angstroms? This '128' refers to on-screen diameter of a sphere, measured in pixels. The job of Sphere3D.java is to render spheres centered at screen coordinates in 3D with the specified diameter. For spheres >=3D maxSphereCache a different rendering routine is used. The cache is one quarter of a sphere, with an int value representing each= pixel. So, a sphere of diameter 128 has a radius of 64. 64=5E2 =3D 4096 *= PI/4 * 4 =3D 12K bytes used that cache entry. > Do you have everything > defined in a single file or are these definitions spread over each of t= he > individual functions? I don't understand the question. In this particular case, the value 128 is local to the Sphere3D implementation. Noone else needs to know about this value. There is reall= y no reason why anyone would ever use it. If we didn't need to worry about old 1.1 JVMs, and we could assume lots o= f memory, then we might bump this value up. > 2) How does your unit notation and RasMol's unit notation compare? > Meaning, for 100 units in RasMol, how many angstroms or units do you ap= ply > in Jmol? I'm not sure I fully understand your question. RasMol defines a special 'RasMol unit' ... there are 250 rasmol units per= angstrom ... an unfortunate design error in my opinion. Jmol fully supports RasMol units, so if you say 'spacefill 250' you will get a 1.0 angstrom radius in RasMol, Chime, and Jmol. I recommend that people writing modern scripts always specify values in decimal values of angstroms, rather than propogating this unfortunate flaw. > 3) This is a question about software, rather than Jmol code. Do you hav= e a > preference for using a specific Java development API such as Eclipse? I use emacs. > Is your source code setup to work with one of these environments? Some other developers (nico + ?) use Eclipse. > Thank you very much for your time, Thanks for your interest in Jmol. Miguel ----- Open Source Molecular Visualization www.jmol.org miguel=40jmol.org ----- |