Martin, I'm afraid you have opened several lines of question within 
the same thread. I am not following all of them.

Version numbers may be critical here

> write COORDS SPT|XYZ|XYZRN|XYZVIB|MOL|PDB "fileName"
> I do the following:
> 
> load pqr::file.pqr // works
> select 1.1         // works
> write "new.pqr"    // does not work
> write COORDS "new.pdb" // works
> write "new.pdb"    // works
> write COORDS "new.pqr" // does not work

That means writing pdb works and writing pqr fails. But, is that Jmol 
12.3? As I said, PQR write is new in 12.3.2
If so, Bob can tell you if there is something worng.


> However, when running the Jmol 11.6.14 applet and entering 'write 
> "new.pdb" ' at the console, i get "File creation failed." 

I am not sure when write pdb was implemented. Maybe 11.6 is too old.
For testing, you can force the use of a different applet version 
without changing your files. See
http://wiki.jmol.org/index.php/Jmol_Applet#Testing_different_applet_ve
rsions

Do that against the latest version and in that way you will see if it 
is a version limitation.




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