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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