Re: [Jmol-users] TopMatch protein structure alignment and superposition web service

[Angel H. <ang...@ua...>]

Markus, congratulations for the site

This looks like a very promising tool. I look forward to having a 
test case where I can test your service.

I have a couple of suggestions:

1.- It would be more useful to generate the display with 2 
models/frames, rather than a pdb file with the 2 chains fused into 
the same model. There are two ways to do that:
a) Insert MODEL / ENDMDL records in the pdb file that contains the 2 
structures.
b) Use Jmol "load files" or "load append" capabilty to load the 2 pdb 
files sequentially (same files you are providing in the download).

That will open up the possibility of easily alternating between both 
structures, or show both, using the "model" submenu in the popup, or 
the animation controls (you could provide some controls for that in 
your page, e.g.:
radio buttons: ( )query ( )target (o)both
and/or:  ( )animate (o)stop.

2.- You mention a potential browser locking problem after several 
sessions; you may be interested in updating the applet, as on recent 
versions a memory leak has been fixed (see the jmol-users list).

3.- Make sure to add your site to the listing at Jmol Wiki

Regards