Am 19.12.16 um 16:37 schrieb Huan Wang: > 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 > <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. > Huan, with the '-J' and '-j' command-line options you must provide the same script commands like interactively. Since command-line arguments in Linux are separated by white-space you have to enclose the script commands in quotes. Like Matt I would also recommend to use 'JmolData.jar' for batch processing of multiple PDB files:
java -jar JmolData.jar -j "write ramachandran 'ramachandran_data.txt'" With single quotes as outer quotes the second double quote seems to get lost in Jmol 14.6.4 and you must add another double quote: java -jar JmolData.jar -j 'write ramachandran "ramachandran_data.txt""' The script commands after '-J' are processed before loading the file, while the script commands after '-j' are processed at the end (also after a script file called with '-s'). Regards, Rolf ------------------------------------------------------------------------------ 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
