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

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"


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2011/10/17 grantaka36 <grantaka36@gmail.com>
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 <speleo3@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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