Dear great masters
I just installed jmol, and it looks very cool, but I haven't
completely understood it yet. I am trying to use it to display a
simple system of red and white spheres.(Actually it is a binary
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
Here the file myscript is given by
select hydrogen;
color atom red;
select helium;
color atom white;
set bonds off
wireframe off;
hbonds off;
But my script doesn't really work, because the atoms do not become
colored. The problem is that the script is applied before I load the
datafile, and therefore the atoms from the datafile arrive too late to
become colored. I can solve this problem by loading the data-file
first and subsequently running my script from the menu, but I would
rather invoke jmol with the script.
Furthermore my script does not turn of all the bonds in the system. I
still get bonds between hydrogen and helium. If the datafile has very
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"
display > bonds -> off
Thanks in advance
Niels
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