Hello Krishna, and welcome to Jmol community
There are probably several ways you can try for your purposes (although I
am not sure to closely understand your setup). Here are some tips:
1. Do not use "zap", as it clears one model before starting to load the next.
Maybe just
load file1.xyz; load append file2.xyz;
or
load files "file1.xyz" "file2.xyz";
http://chemapps.stolaf.edu/jmol/docs/#loadappend
http://chemapps.stolaf.edu/jmol/docs/#loadfiles
2. If the atoms and bonds are the same in all models, you can try
load trajectory
but probably that may not be done with several files, only with a multimodel
file
http://chemapps.stolaf.edu/jmol/docs/#loadtrajectory
3. If you are calculating the coordinates, there is no need to save files, you
could try loading the data using the "data" or "load data" commands
http://chemapps.stolaf.edu/jmol/docs/#loaddata
4. It is indeed possible to change atom coordinates of the current model
inside Jmol, avoiding the need to load a second, third... files. For this, you
access and set the atom properties (x, y, z, xyz, atomX, atomY, atomZ). See
http://chemapps.stolaf.edu/jmol/docs/#atomproperties
Example:
{atomno=3}.x = 0.123;
{atomno=3}.y = 2.03;
{atomno=3}.z = -0.31;
I am quite sure if you explore those you will find your solution. Jmol
scripting
is very flexible and powerful.
Good luck and let us know the outcome,
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