Hello Sam, and welcome

(This rather belongs into jmol-users list)


>      I'm emailing to ask a few questions about JMol. From what I've 
> found on your emailing archives, it seems like it is possible to load 
> multiple structures at once, but how exactly would one do that using the 
> frame commands? 

You use the "load" command. The "frame" command controls display of one 
or another, later on.

in brief, 
  load files "file1.pdb" "file2.pdb"
for details, see http://chemapps.stolaf.edu/jmol/docs/#loadfiles


> In addition, I was wondering if it was possible in JMol 
> to manipulate a structure's coordinates and then save those coordinates.

Yes, it is possible. There are a few ways to move atoms, like
"rotateSelected" and "translateSelected" 
They can also be moved with the mouse, after activating the proper mode 
(see the "picking" command and more).

Then, you use the "write coords" command

Everything at http://chemapps.stolaf.edu/jmol/docs
though it takes some time to master those issues

Good luck!


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