Re: [Jmol-users] How to align more than two protein structures

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

Hello Justin 

In brief, you cannot do what you want in Jmol. Jmol uses the atom 
coordinates in the file, so if you load several files in the same 
window you cannot move them separately (well, there are the recent 
translateSelected and rotateSelected commands, so maybe you can, but 
it is not a very versatile movement and these are not frequently 
used, so you will have to find out by yourself)

Latest versions of Rasmol can do that (no applet version, just 
application).

Another thing you can do is to insert 3 applets in a web page, and 
load one file into each. Then you have independent movement on each 
molecule.

To achieve what you want in a single applet (but still without 
independent rotation of each single molecule) you would need to 
combine the 3 files into one and edit it so that each molecule gets 
new coordinates. This sort of thing can be done e.g. in Accelrys 
Discovery Studio Visualizer. Then, save back the result into a new 
pdb file wwhich you would open in Jmol.
More powerful software like DeepView will let you do the same and 
also do the alignment of the molecules for you, although it takes 
some effort to learn how to do that.

Hope you can find a solution