Sorry, I copied the wrong piece of code in my former reply. This is the correct
way:
Hello, Huan
You are in the right drection.
> Actually, I found a very brief introduction in Jmol Wiki website, where
listed some commands for loading PDB file and
> running script in command line. However, I did not see any command for
saving data.
Not specifically to save data, but it's the same method for any Jmol
command or script.
> write ramachandran "OUTPUT_FILE_NAME"
That is a Jmol script
tells you can use
Jmol.jar fileName -J script_commands -s scriptFileName -j
script_commands
So it's probably a question of quotes; please try this way:
Jmol.jar PDB_FILE -J '
write ramachandran "OUTPUT_FILE_NAME"; '
or
Jmol.jar PDB_FILE -J "
write ramachandran 'OUTPUT_FILE_NAME'; "
or, when the filemname is not conflictive (ie it does not use spaces or
nonASCII characters) you can omit the quotes:
Jmol.jar PDB_FILE -J "
write ramachandran OUTPUT_FILE_NAME; "
If that fails, or if it is more convenient for you, you can save the
script in a
text file, e.g. named MYSCRIPT.TXT and then
Jmol.jar PDB_FILE -s MYSCRIPT.TXT
Jmol.jar PDB_FILE -s "MYSCRIPT.TXT"
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