Hello Amos, and welcome to Jmol!
Your intention is rather singular, but there is a good chance that Jmol can do
it. There is
much power below the hood.
If I get it right, you want to produce frames that contain only changes in some
atoms. And
changes in their identities rather than in their coordinates (which is the most
common
situation).
You will have to use scripting for this.
These are the basic elements than can lead to implementing your needs:
{atomno=3}.element = 29
will convert the 3rd atom in your model into Cu (using atomic nr. = 29)
data "append" (etc.)
command allows to create a new frame with inline data
Now the issue is how to put a copy of the atoms in that new frame, then apply
the atoms
change.
You can create models inline, but I see that will not reduce your load, as
you'd have to
create the full set of 400.
So maybe that's not the right course. It depends on how you need to use the
models, maybe
you can script the changes but use a single frame. Do you want an animation? Do
you want
to be able to run forward and backward, step by step?
And in any case, have you tried to use
load trajectory
? That reduces the load and speeds the animation, but the multiframe file
needs to have
the same atoms in every frame, so it may be precisely what you don't have.
Let's keep the discussion. Please provide some more details
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