Am 19.12.16 um 18:13 schrieb Rolf Huehne: > 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'" > Sorry, I forgot the PDB filename which would be placed at the end of the command-line:
java -jar JmolData.jar -j "write ramachandran 'ramachandran_data.txt'" PDB_FILE 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
