Hello Aida
I've done a little bit of research.

1. The "data" command works. You need to give it atom data in one of the 
supported formats (xyz is the simplest).
2. I enquired about using "data" to append data rather than substitute the 
current model and it can be done, but there is some bug. However, the 
mechanism for foing that is there.
3. Once the new atoms are added, you can move them (or the old ones) 
using the mouse after "set dragSelected true"

So, it's not going to be very user-friendly, but it can be done. What is not 
there is the way to insert a new atom using the mouse (that's tricky anyway 
since you see it in 2D but it is 3D. How would you define the z coordinate of 
the new atom?)
If you can code Java, then there is the possibility to implement a nicer way, 
something like a first step to make Jmol an editor. Doing that well is 
probably hard and non-trivial; many things need to be taken care of. 
Anyway I would be willing to assist you, but I cannot write Java.

I would propose that first we start with a Jmol applet in a web page and try 
to define and implement what you want: load a model (or not), add some 
atoms, move them around with the mouse. Does it sound ok to you?


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