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 <spel...@users.sourceforge.net>:
> 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
>
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