Re: [Jmol-users] Displaying colored spheres without bonds (Please help with script)

[Angel H. <ang...@ua...>]

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!