From: Miguel <mt...@mt...> - 2003-11-04 13:30:59
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> Hi again, the recent discussion I joined was about .pdb files and the > "set connect" script command. Miguel said that when there is bond > information in a file, Jmol should stick to it, and I wonder if this > would apply to all formats. Jmol is a visualization program, not a calculations program. If there is connectivity information in a file then Jmol will faithfully render the molecule using that connectivity information. This is independent of file type. (With the caveat that CONECT records are *currently* not used for .pdb files ... this is considered a bug). If the file contains no connectivity information then Jmol applies an algorithm to generate bond links. The current algorithm is quite simple, and uses covalent radii of the two atoms and a 'tolerance' factor. This algorithm will probably change in the future. > I got a colleague who is still working with CaGe to send me two > samples of the CML format that I made our program send to the Jmol > applet. Note the "convention" in the third lines. I wonder what a > current version of the applet would make of them? Unfortunately, I don't know anything about CML. I have been focusing on the scripting and rendering aspects of Jmol. This portion of the code is completely independent from the File IO. One of the other developers will need to take a look at your CML files. > What the display > should be with the "unchemical" file I don't know, I'm afraid - this > is not a question of the "what do you see" style but rather one > for the developers: what would Jmol make of the data in these > files, and would you be willing to make it adhere strictly to the > bonds and atom positions? If the coordinates are in the file *and* the file reader uses them then Jmol should display it exactly as prescribed by the file. I know that if you have a .mol file then the coordinates will be respected. For example, we have a file samples/jmol.mol which is a 'dot-matrix' representation of the letters JMOL using carbon atoms. Looks fine on the screen. Miguel > > Sebastian |