Hi Brian,
Thank you very much for your great job!
Best,
XH
On 06/07/2017 11:51 PM, Brian Smith wrote:
> Hi XH,
>
> Ah yes - if you're using the precompiled analysis, it will be Tk8.6.
>
> I've just added a HowTo for compiling your own (it's easy) Analysis and installing ARIA on CentOS 7 to the CCPNWiki
>
> https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/centos-7-x-standard-installation
>
> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
>
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Xuehui Liu [[log in to unmask]]
> Sent: 07 June 2017 01:21
> To: [log in to unmask]
> Subject: Re: Can not close aria GUI
>
> Hi Brian,
>
> Thank you. The tk version for the system when I 'rpm' to ask is
> 'tk-8.5.13-6.el7.x86_64'. I thought Ben meant the tk8.6 included in the
> ccpnmr.
>
> By the way, the 'Shift+Left Mouse' worked. Thanks a lot!
>
>
> Best,
>
> XH
>
>
> On 06/06/2017 07:09 PM, Brian Smith wrote:
>> Hi XH,
>>
>> Glad Ben's suggestion worked, though I'm curious as to why you are seeing different behaviour to me. Are you actually using Tk 8.6? The default on CentOS 7 is 8.5.13.
>>
>> I don't think you need to worry about the PyOS_InputHook warning.
>>
>> For all this aria specific stuff you should probably move the discussion to the aria group on yahoo -
>>
>> https://groups.yahoo.com/neo/groups/aria-discuss/info
>>
>> but for editing the input fields that go grey when you click on them do Shift+Left Mouse to unlock them.
>>
>>
>> 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 Xuehui Liu [[log in to unmask]]
>> Sent: 06 June 2017 09:12
>> To: [log in to unmask]
>> Subject: Re: Can not close aria GUI
>>
>> 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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