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 http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options 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 'ramachandran "OUTPUT_FILE_NAME"; ' or Jmol.jar PDB_FILE -J "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 "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" ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
