Hi Ravi Yes. there is a command to fix a certain frame/model so that you can see it overlayed with any other you choose: set backgroundModel (integer >= 1)
Sets a particular model or animation frame to be fixed in place during
an animation
<http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#animation> or
when displaying models loaded
<http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#load> from a
multi-model file. set backgroundModel 0 turns this feature off. Certain
restrictions apply to scripts when a background model is displayed; in that
case it may be important to turn the model off and then back on during selected
scripting.
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