Hi Chris

Adding to Rolf's reply:

You have two independent commands to take care of:

1. "hide" and "display" control visibility across all frames/models, allowing 
to 
control part of the models (e.g. "hide water" or "hide nucleic")

2. "frame" controls which frame/model is shown

So it is a combination of both.

If you want to display models in both files together, you need "frame all" and 
then you can use "display" attached to your checkboxes.

Or do not use "hide" or "display" and just use "frame" in the checkboxes.

load files "a.pdb" "b.pdb";
and 
load "a.pdb"; load append "b.pdb";
are equivalent and, by default, only the last model will be shown --until you 
use "frame all"

> >     but in my case (http://www.ccpem.ac.uk/jsmol_test/test2.html) 1crn 
does not get shown e.g. clicking the 'hide 1.1' button does hide 1crn, 
showing that 2ol9 is not there.  Only if the checkbox is clicked does 2ol9 
appear.

Your "model 0" is the same as "frame 0" or "frame all". So it is working to 
superimpose both files, as long as you have not clicked "hide 1.1"




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