Hi CY and Jared, Jared, CY is actually right that MacPyMOL won't run if you're not logged in to the Mac desktop. I assume in your test, you were logged in on the imac (WindowServer running for your user).
For this use case, we now provide the "Mac alternative X11-only build" (current: "pymol-v1.7.6.1-Darwin-x86_64.tar.gz") which is built like on a unix system, linked to X11 graphics (requires XQuartz) instead of OSX Cocoa. This version works without a WindowsServer in command line "-c -q" mode. CY, please give that version a try. Cheers, Thomas On 29 May 2015, at 12:35, Sampson, Jared <jared.samp...@nyumc.org> wrote: > 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> 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (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
