Hi CY - If you're using the -c flag, you shouldn't need a windowing system at all. The following works for me between a MacBook Air and an iMac, both running 10.9.5, with MacPyMOL 1.7.6.0 installed on the iMac.
### begin shell ### (macbook-air)~ › ssh jared@imac Password: Last login: Fri May 29 10:37:12 2015 from macbook-air (imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd "fetch 3opl, async=0; save tmp.png" PyMOL>fetch 3opl, async=0; save tmp.png HEADER HYDROLASE 01-SEP-10 3OPL TITLE ESBL R164H MUTANT SHV-1 BETA-LACTAMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE SHV-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIT-2; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 4 symmetry operators. CmdLoad: "./3opl.pdb" loaded as "3opl". Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.). ScenePNG: wrote 640x480 pixel image to file "tmp.png". (imac)~ › exit logout Connection to imac closed. (macbook-air)~ › ### end shell ### The file ~/tmp.png is created on the iMac. I also used -k to prevent PyMOL from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands. If you're running a .pml script, you don't need to include -d, just the path to the script (which must be on the remote machine). As you noted, when it runs I see the MacPyMOL application icon pop into the Dock on the iMac and then disappear as soon as the script finishes. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 28, 2015, at 11:28 AM, Yu Chen <che...@umbc.edu<mailto:che...@umbc.edu>> wrote: Hello, I am trying to run MacPyMOL in command line mode with "-c -q" option. While directly logged in to the computer, it works. But if I ssh into the computer (even with X11 forwarding enabled), it fails with some errors about connecting to WindowServer And I can tell it actually tried to launch the GUI very briefly, then returned to the command line to process the scripts. Is this right? Can I run it remotely on another computer just from pure command line. Thanks. CY ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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