Hello, Nanthini
Clearing models once and again could lead you into memory use problems,
but you can certainly try.
The command you need to clear a whole model loaded is
zap file
zap model
See http://www.stolaf.edu/academics/chemapps/jmol/docs/#zap
Example:
load mol1.pdb;
load append mol2.pdb;
zap file=1; //will remove mol1.pdb
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