Hello, Niels > Lennard-Jones liquid with around 10000 particles). I am writing a > script, but I cannot turn of all the bonds and applying the colors > right. I invoke jmol in the following way > > jmol -s myscript datafile.xyz
I have no experience with the command line for the app (I use the applet), but - I agree with you that it seems the script should go after the file load, but Jmol doc says the file goes last. - You can try to call the file from within the script: load datafile.xyz select hydrogen; color atom red; select helium; color atom white; set bonds off wireframe off; hbonds off; and then jmol -s myscript > Furthermore my script does not turn of all the bonds in the system. I > still get bonds between hydrogen and helium. "wireframe off" should be enough to turn bonds representation off. On a second look, your scriptmay be failing because you are applying commands adter selecting certain atoms, so it only applies to these. You should insert a "select all" after "color atom white;" > densely packed spheres, then I get a lot of errors called "maximum > auto bond count reached", and the file takes a lot of time to load. I > can fix this problem by choosing "don't compute bonds" from the menu > before I load the datafile, but I would like to fix the problem by > invoking jmol with a script. Does the scripting language of jmol offer > equivalents of the following menu entries? > > edit -> preferences -> bonds -> "don't compute bonds" I'm not sure that "set bonds off" has to do with this. Surely Miguel or the other more technical folks can illustrate you about auto bonding. Anyway, try it again after fixing the select. Good luck! ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
