Huan, You can add a line to your .profile or your .bashrc to recognize an alias to run Jmol.
For example, on my mac, I have edited my .profile to include: alias jmol144="java -jar /Applications/jmol-14.4.0_2015.12.02/Jmol.jar” This line means that typing jmol144 opens Jmol. Note that if you are processing a lot of files, you may want JmolData.jar instead, which will run your scripts without graphical overhead. Matt On Dec 19, 2016, at 10:37 AM, Huan Wang <huan.w...@mail.huji.ac.il<mailto:huan.w...@mail.huji.ac.il>> wrote: 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 . ------------------------------------------------------------------------------ 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<mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ 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
