Hello Liu

Can you be more specific? That would help.

By "multiple layer", do you mean several models (frames) are loaded 
together? Or something else?

>  http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP does not 
behave where not all the atoms and bonds in protein are cartooned. 

Which parts of the protein are not displayed? I just loaded the pdb into Jmol 
and I see no problem in the cartoon.


Finally, this will not affect, but for your information
you do not need to repeat  "set appendNew true",
and "zoom" applies to all models at the same time, so no need to repeat it.



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