Dear Jmol developers and users,
I am a newbie to Jmol and I have a question on running Jmol in Linux
command line.
Previously, when I prepared Ramachandran plot, I used Jmol interface to
open PDB file and typed command in Jmol console as:
*write ramachandran "OUTPUT_FILE_NAME"*
That was very low efficient especially when dealing with large amount of
PDB files. If Jmol could run in command line in Linux system with Bash
Shell script, that would be perfect.
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.
http://wiki.jmol.org/index.php/Jmol_Application
I tried to use
Jmol -n PDB_FILE -J ramachandran "OUT_PUT_FILE_NAME" -x
Howeve, it does not save data.
I also tried
Jmol -n PDB_FILE -J ramachandran -w "OUT_PUT_FILE_NAME" -x
It saved the image file, not data.
other trials were:
Jmol -n PDB_FILE -J ramachandran > "OUT_PUT_FILE_NAME" -x
Jmol -n PDB_FILE -J write -j ramachandran "OUT_PUT_FILE_NAME" -x
However, none of them worked as I expected...
It would be greatly appreciated if anyone could help me.
Thank you very much.
Best wishes,
Huan
.
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