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Re: [PyMOL] how to activate pymol from remote server
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From: Troels E. L. <tl...@gm...> - 2011-10-17 08:09:52
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*This does not seem to be an issue of Pymol.* If you can't open a display to any program, like "gedit", you are not doing it right. Get an open display to any program, and then try Pymol. Here is a start to do it. *http://x.cygwin.com/docs/ug/using-remote-apps.html*<http://x.cygwin.com/docs/ug/using-remote-apps.html> You NEED to pass *-Y* to the ssh program. ssh *-Y* -l (loginname) (hostname) But please come back again, if have problems regarding Pymol. If you only neeed Pymol scripting, and no display, you can check here: http://www.pymolwiki.org/index.php/Launching_PyMOL#Running_PyMOL_in_batch_mode "pymol -cq" Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/10/17 grantaka36 <gra...@gm...> > Hi Thomas, > > I appreciate your advice very much, testing and cannot find green > signal yet as [2]. For now, what I want to do is [1], so please give > me, if any enough, advice or workaround. If information might be > inadequate, please contact me. > > [1] > >> how to activate pymol from remote server? > >> i.e. how to start pymol in [S] by scripting from [C] > > Sorry for lack of information, what all I'd like to do is: > - Scripting in [C] (on Cygwin or telnet over Command Prompt etc. > welcome), which includes login procedure to [S] by 'ssh -l (loginname) > (hostname)' > - pymol GUI open in [S]'s window (not in [C]) > > I wonder, if even in this case X-forwarding is needed. > > [2] > > do you have a X server running on Windows? It works for me with Cygwin > with > > installed X and GL libraries (but it's not very convenient because quite > > slow). > > > > ssh -Y linuxserver > > pymol > > Windows [C] didn't have X-server so I installed Xming 6.9.0.31 and > kept running, 'pymol' returns: > | freeglut (pymol): failed to open display '' > | PyMOL: abrupt program termination. > > Another command returns: > | $ gedit (one shell script).sh > | (gedit:3887): Gtk-WARNING **: cannot open display: > | (returned empty) > | $ > > | $ grep X11Forwarding /etc/ssh/sshd_config > | X11Forwarding yes > | $ grep X11DisplayOffset /etc/ssh/sshd_config > | X11DisplayOffset 10 > > So, I think X-forwarding setting done but not all of 'install X and GL > libraries' might be intalled yet. > > > Regards, > Masataka > > > 2011/10/15 Thomas Holder <sp...@us...>: > > Hi Masataka, > > > > do you have a X server running on Windows? It works for me with Cygwin > with > > installed X and GL libraries (but it's not very convenient because quite > > slow). > > > > ssh -Y linuxserver > > pymol > > > > If pymol is set up on that linux server correct and runs there by just > > typing "pymol", it should as well from an X-forwarded ssh connection. No > > need to export variables. Don't use the -R and -display arguments. > > > > Cheers, > > Thomas > > > > > > grantaka36 wrote, On 10/14/11 07:35: > >> > >> Dear list members, > >> > >> Would you please tell me the way, how to activate pymol from remote > >> server? i.e. how to start pymol in [S] by scripting from [C] > >> > >> ------------------------------ > >> - From Windows client [C], SSH2 logging in to the remote server [S] > >> (Linux x64, Ubuntu 10) > >> - [S] > >> -- installed PyMOL 1.2 r2, PATH includes '/usr/bin/pymol' so only > >> 'pymol' entering enable to activate pymol GUI > >> -- 'python' returns > >> -- Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) > >> -- [GCC 4.4.5] on linux2 > >> - [C] > >> -- first trying the following: > >> PYMOL_PATH=/usr/bin/pymol > >> HOST_ID=`uname -n` > >> pymol -R -display:${HOST_ID}:0.0 > >> -- returns: > >> Traceback (most recent call last): > >> File "/usr/lib/python2.6/runpy.py", line 122, in _run_module_as_main > >> "__main__", fname, loader, pkg_name) > >> File "/usr/lib/python2.6/runpy.py", line 34, in _run_code > >> exec code in run_globals > >> File "/usr/lib/pymodules/python2.6/pymol/__init__.py", line 495, in > >> <module> > >> invocation.parse_args(pymol_argv) > >> File "/usr/lib/pymodules/python2.6/pymol/invocation.py", line 251, > >> in parse_args > >> options.stereo_mode = int(av.pop()) > >> IndexError: pop from empty list > >> ------------------------------ > >> > >> By referring, > >> > >> > http://www.pymolwiki.org/index.php/Launching_PyMOL#Launching_PyMOL_from_an_external_application > >>> > >>> If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, > >>> then you can launch PyMOL from an external Python program > >> > >> But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY > >> > >> > >> Regards, > >> Masataka > > > > -- > > Thomas Holder > > MPI for Developmental Biology > > Spemannstr. 35 > > D-72076 Tübingen > > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
