Re: [Jmol-users] Superimpose Models

[Rolf H. <rh...@fl...>]

Lin Yi wrote:
> Hi all,
> 
> I'm wondering whether there is a way to superimpose models in Jmol.  Say I
> have four models (1.1, 2.1, 3.1, 4.1) and I want to show 1.1 and 3.1 at the
> same time or maybe any other combination of the four models.  I tried to use
> the model script but it would either go to a specific model (1.1) or display
> a range of models (1.1-3.1).  What I wanted to do is to display another
> model on top of the model currently displaying in the applet.  Can anybody
> help me?  Thanks.
> 

To display any combination of models you can use the 'display' and
'hide' commands (http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#display).

In your example you could either use

  frame all; display 1.1 or 3.1

or

  frame all; hide 2.1 or 4.1

The command 'display' displays everything that matches the atom
expression provided within the command. And it also hides everything
that does not match it.

Similarly the command 'hide' hides everything that matches the atom
expression provided within the command. And it also displays everything
that does not match it.

This behaviour is not quite what you might expect naively from the
command names. But it was designed to work similarly as the 'select'
command of Jmol, which also deselects everything that is not matching
the atom expression provided within the command.

And you must be careful if you mix the 'frame' or 'model' command with
the 'display' or 'hide' commands because they work totally independent.
(e.g.: "frame 1.1; display 3.1" would result in displaying nothing until
the command "frame 3.1" or "frame all" would be provided)

Regards,
Rolf