Dear Benjamin,
Thank you very much! It worked!!
Now I got another problem with aria2 GUI. I could not input in some
fields, for example, the "Disulfide bridges (covalent)" and the "Job
Manager".
When I click on the fields, they just turned grey. I have to edit the
project xml file to get these fields filled.
And, I am sorry there are so many questions, I got the following warning
when running aria2:
WARNING [Protocol]: Traceback (most recent call last):
File
"/home/xhliu/programs/aria2.3/src/py/aria/Protocol.py
", line 1316, in dumpIteration
self._dump_rms(peak_list, iteration.getNumber())
File
"/home/xhliu/programs/aria2.3/src/py/aria/Protocol.py
", line 1244, in _dump_rms
rp.go()
File
"/home/xhliu/programs/aria2.3/src/py/aria/RmsReport.p
y", line 379, in go
self.plotPsReport()
File
"/home/xhliu/programs/aria2.3/src/py/aria/RmsReport.p
y", line 318, in plotPsReport
self.plotAllEps()
File
"/home/xhliu/programs/aria2.3/src/py/aria/RmsReport.p
y", line 334, in plotAllEps
self.plot2dRmsMap(self.eps_map)
File
"/home/xhliu/programs/aria2.3/src/py/aria/RmsReport.p
y", line 288, in plot2dRmsMap
rcParams['numerix'] = 'numpy'
File "/usr/lib64/python2.7/site-packages/matplotlib/
__init__.py", line 705, in __setitem__
See rcParams.keys() for a list of valid
parameters.' %
(key,))
KeyError: 'numerix is not a valid rc parameter.See
rcParams.keys() for a list of valid parameters.'
WARNING [Protocol]: Error during RMS analysis/graphics generation.
Best regards,
XH
On 06/06/2017 03:22 PM, Benjamin Bardiaux wrote:
> Hi,
>
> certainly comes from python2.7/Tk8.6 that returns unicode strings.
>
> Simple fix:
>
> Edit aria2.3/src/py/aria/gui/gui.py
>
> and change the offending line:
>
> s['geometry'] = self.root.winfo_geometry()
>
> by
>
> s['geometry'] = str(self.root.winfo_geometry())
>
> Cheers,
>
> Benjamin
>
> On 06/06/2017 02:22 AM, Xuehui Liu wrote:
>> Hi Brain,
>>
>> I've tried your suggestion and got this:
>>
>>
>> MESSAGE [GUI]: [Errno 2] No such file or directory:
>> '/home/xhliu/.aria_gui'
>>
>> MESSAGE [GUI]: Could not load settings (~/.aria_gui).
>>
>> MESSAGE [GUI]: Using default settings.
>>
>> Exception in Tkinter callback
>> Traceback (most recent call last):
>> File
>> "/home/xhliu/programs/ccpnmr/python2.7/lib/python2.7/lib-tk/Tkinter.py",
>> line 1532, in __call__
>> return self.func(*args)
>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line 1287,
>> in <lambda>
>> command = lambda s = self: s.exit())
>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line 997,
>> in exit
>> s['geometry'] = self.root.winfo_geometry()
>> File "/home/xhliu/programs/aria2.3/src/py/aria/Settings.py", line 682,
>> in __setitem__
>> entity_type, err_msg))
>> File "/home/xhliu/programs/aria2.3/src/py/aria/ariabase.py", line 211,
>> in error
>> raise exception, msg
>> EntityValueError: USER ERROR <aria.gui.gui.GUISettings> File
>> "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line 997 in exit
>> GUISettings: Value "1000x800+12+70" for entity "geometry" (String) is
>> invalid.
>> String excepted.
>>
>> "Always send" option
>>
>> And I also run the aria2 check.py and got the following message, could
>> that be the reason? I think I didn't get any gtk problem when aria2 was
>> installed. Should I re-install aria2 and try?
>>
>> Python version ok.
>> Numpy module ok (numpy)
>> Tkinter and Tix modules...
>> Tkinter imported (Tk version 8.500)
>> Tix imported.
>>
>> CCPN distribution: ok.
>> Format converter: ok.
>> Anaysis: ok.
>> /usr/lib64/python2.7/site-packages/gtk-2.0/gtk/__init__.py:122:
>> RuntimeWarning: PyOS_InputHook is not available for interactive use of
>> PyGTK
>> set_interactive(1)
>> Matplotlib module (optional) ok.
>>
>>
>> Thank you!
>> Best regards,
>>
>> XH
>>
>> On 06/05/2017 04:48 PM, Brian Smith wrote:
>>> It's an odd one for sure.
>>>
>>> The error comes from a
>>>
>>> self.root.winfo_geometry()
>>>
>>> call which should be bullet proof. Surely the developers would not
>>> have embedded any hard limits in there?
>>>
>>> The default setting in the aria code is
>>>
>>> 'geometry': '1000x800+11+33',
>>>
>>> so the 3 digits idea can't be right.
>>>
>>> I'm running on CentOS 7 and don't see that problem (yet).
>>>
>>> the ARIA GUI does park some defaults in a . file in your home
>>> directory - maybe that is corrupted? Try
>>>
>>> mv ~/.aria_gui ~/.aria_gui.old
>>>
>>> and then try aria again?
>>>
>>>
>>> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow
>>> ac uk
>>> Institute of Molecular, Cell and Systems Biology & School of Life
>>> Sciences,
>>> College of Medical, Veterinary & Life Sciences,
>>> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
>>> Tel: 0141 330 5167/6459/3089
>>> ----------------------------------------------------------------------
>>> The University of Glasgow, charity number SC004401
>>>
>>> ________________________________________
>>> From: CcpNmr software mailing list [[log in to unmask]] on behalf
>>> of Wayne Boucher [[log in to unmask]]
>>> Sent: 05 June 2017 09:37
>>> To: [log in to unmask]
>>> Subject: Re: Can not close aria GUI
>>>
>>> OK, it looks like the y is ok now so hopefully it’s just the width
>>> (1311) that you need to reduce. Likely Tkinter doesn’t like anything
>>> more than three digits in any of width / height / x / y.
>>>
>>> Wayne
>>>
>>>> On 5 Jun 2017, at 09:31, Xuehui Liu
>>>> <[log in to unmask]> wrote:
>>>>
>>>> Hi Wayne,
>>>> Thank you very much for the prompt reply. I've tried your suggestion
>>>> and got the same error, some think like:
>>>>
>>>> Traceback (most recent call last):
>>>> File
>>>> "/home/xhliu/programs/ccpnmr/python2.7/lib/python2.7/lib-tk/Tkinter.py",
>>>>
>>>> line 1532, in __call__
>>>> return self.func(*args)
>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line
>>>> 1287, in <lambda>
>>>> command = lambda s = self: s.exit())
>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line
>>>> 997, in exit
>>>> s['geometry'] = self.root.winfo_geometry()
>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/Settings.py", line
>>>> 682, in __setitem__
>>>> entity_type, err_msg))
>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/ariabase.py", line
>>>> 211, in error
>>>> raise exception, msg
>>>> EntityValueError: USER ERROR <aria.gui.gui.GUISettings> File
>>>> "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line 997 in
>>>> exit
>>>> GUISettings: Value "1311x853+450+188" for entity "geometry" (String)
>>>> is invalid.
>>>> String excepted.
>>>>
>>>> "Always send" option
>>>>
>>>>
>>>>
>>>> I noticed that the geometry values changed, but I still cannot close
>>>> the GUI.
>>>>
>>>> I do have two screens, one on the top of the other. How could I deal
>>>> with this problem if I still want to use two screens?
>>>>
>>>> Thank you!
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> XH
>>>>
>>>>
>>>> On 06/05/2017 03:26 PM, Wayne Boucher wrote:
>>>>> At a guess, Tkinter is unhappy with one or more of the geometry
>>>>> values being so large (screens are a lot bigger than they used to
>>>>> be), I’m not sure if it’s the width or the y location (or both) that
>>>>> is triggering this. Try moving the window to the first screen (if
>>>>> you have more than one screen) or towards the top (if only one
>>>>> screen) and maybe make it a bit less wide, and see if that helps.
>>>>>
>>>>> Wayne
>>>>>
>>>>>> On 5 Jun 2017, at 08:16, Xuehui Liu
>>>>>> <[log in to unmask]> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am using CCPNmr 2.4.2 and aria2.3.1 on a CentOS 7.
>>>>>>
>>>>>> When I was setting up a calculation in the ccpnmr, I opened a aria
>>>>>> GUI. After I checked the parameters, I could not close the GUI.
>>>>>> When I did so, I got the following message:
>>>>>>
>>>>>> Exception in Tkinter callback
>>>>>> Traceback (most recent call last):
>>>>>> File
>>>>>> "/home/xhliu/programs/ccpnmr/python2.7/lib/python2.7/lib-tk/Tkinter.py",
>>>>>>
>>>>>> line 1532, in __call__
>>>>>> return self.func(*args)
>>>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line
>>>>>> 1287, in <lambda>
>>>>>> command = lambda s = self: s.exit())
>>>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line
>>>>>> 997, in exit
>>>>>> s['geometry'] = self.root.winfo_geometry()
>>>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/Settings.py", line
>>>>>> 682, in __setitem__
>>>>>> entity_type, err_msg))
>>>>>> File "/home/xhliu/programs/aria2.3/src/py/aria/ariabase.py", line
>>>>>> 211, in error
>>>>>> raise exception, msg
>>>>>> EntityValueError: USER ERROR <aria.gui.gui.GUISettings> File
>>>>>> "/home/xhliu/programs/aria2.3/src/py/aria/gui/gui.py", line 997 in
>>>>>> exit
>>>>>> GUISettings: Value "1311x853+202+1199" for entity "geometry"
>>>>>> (String) is invalid.
>>>>>> String excepted.
>>>>>>
>>>>>> Any idea? Thank you very much!
>>>>>>
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> XH
>
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