Thanks for your answer. I' ll try the second option for hiding the name in
the popup.
For similarity I thought about using a BLOSUM matrix, but don't know how to
set it up.
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>
http://wiki.jmol.org/index.php/Custom_Menus
For (2), see
set disablePopupMenu
set hideNameInPopUp
under
<http://chemapps.stolaf.edu/jmol/docs/#setvisibility>
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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