Annika Kreuchwig wrote:

> First: I was wondering if it is possible to change the pop-up menu or to
> avoid that the user is able to download the structure which is provided in
> Jmol? 

Yes,both. For (1), see 
http://wiki.jmol.org/index.php/Custom_Menus
For (2), see
 set disablePopupMenu
 set hideNameInPopUp 
under 
http://chemapps.stolaf.edu/jmol/docs/#setvisibility

Note, however that since you are coding the whole thing in the html, 
the user will alwasy be able to find the url for the structure file 
and download it, even if not directly from within Jmol. Remember, 
everything you put on the web is accesible.

 
> Second: Is there a possibility to search a structure for motifs? Like DRY
> motif but to recognize also similar motifs like ERY, using similarity
> matrices for example? I just read how you select a motif (select
> within("DRY", *)) but it would be even more interesting for me, if it is
> possible to search for similar motifs. 

The problem is how "similarity" is defined; you will have to do that 
yourself, Jmol cannot do it since it is not a general problem.
For ex., just do
select within("DRY", *),within("ERY", *)


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