[Chimera-users] kill graphics windows after crash: it happend again

Tue Oct 13 22:46:13 PDT 2020

Hi,

     it happened again: after the message that the loading of a map was 
very slow chimera got stuck and I cannot get rid of its windows. If I 
open something else it overlays the chimera windows. ps -ealf|grep 
chimera just shows me a single process, namely the one of ps. Please see 
attached screenshots! For the moment I can push the chimera windows out 
of view but I cannot close them. I possibly have to reboot again....

thanks for hints, bw Dieter

------------------------------------------------------------------------
Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail: dieter.blaas at meduniwien.ac.at
------------------------------------------------------------------------

On 06.10.2020 04:24, Dieter Blaas wrote:
> Dear Tom and Eric,
>
>      thank you! In the meantime I finally decided to reboot! The 
> situation is difficult to reproduce but happens once within several 
> months either because of a very slow network (when we experience 
> general problems with the server) or because there is something wrong 
> in a saved and then modified session file. However, I cannot exclude 
> that the cause is something else! Fact is that I then cannot close any 
> of the chimera windows, they simply stay open despite having killed 
> all related processes.
>
> Could it be caused from working remotely over VNC? But when restarting 
> the VNC server and then restarting Chimera it usually happens again! 
> When I observe it next time I'll try "kill -s KILL process_id" and 
> also take screen shots. As I am the only user rebooting is not a problem!
>
> best, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: dieter.blaas at meduniwien.ac.at
> ------------------------------------------------------------------------
>
> On 05.10.2020 20:58, Tom Goddard wrote:
>> Hi Dieter,
>>
>>    I am curious what you are using in Chimera that uses the network 
>> when you have to kill it?  I tried fetching a large EM map (10860, 
>> ~500 Mbytes) from EMDB with File / Fetch by ID on Mac, then I turned 
>> off my wifi part way through and tried ctrl-C in the shell where I 
>> had started Chimera 1.14.  One try it exited the program, and the 
>> second try it gave a keyboard interrupt message and Chimera was no 
>> longer hung.  If I left my wifi on then the stop button in the lower 
>> left corner of the Chimera window at the front of the status messages 
>> successfully stopped the download.  But if I disconnected the wifi, 
>> that stop button didn't work.
>>
>>    Maybe you are on Linux or maybe Chimera is hung on some web 
>> service you are using like BLAST....
>>
>>     Tom
>>
>>
>>> On Oct 5, 2020, at 11:30 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>>
>>> Hi Dieter,
>>>     Instead of "kill process_id" try "kill -s KILL process_id".
>>>
>>> --Eric
>>>
>>>     Eric Pettersen
>>>     UCSF Computer Graphics Lab
>>>
>>>> On Oct 4, 2020, at 9:05 AM, Dieter Blaas 
>>>> <dieter.blaas at meduniwien.ac.at> wrote:
>>>>
>>>> Hi,
>>>>
>>>>     please forgive me when this question is not directly related to 
>>>> Chimera: Sometimes Chimera becomes unresponsive because of a slow 
>>>> network connection. When I then try exiting it or killing it with 
>>>> <ctrl> c from the terminal I used to start it or killing the 
>>>> chimera-related process as shown with ps -ealf|grep UCSF or grep 
>>>> chimera the chimera windows remain and I cannot remove them. Any 
>>>> way of doing so?
>>>>
>>>> Thanks for hints, best, Dieter
>>>>
>>>> ----------------------------------------------------------------------- 
>>>>
>>>> Dieter Blaas,
>>>> Max Perutz Labortories
>>>> Medical University of Vienna,
>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>> Dr. Bohr Gasse 9/3,
>>>> A-1030 Vienna, Austria,
>>>> Tel: 0043 1 4277 61630,
>>>> Mobile: 0043 699 1942 1659
>>>> e-mail: dieter.blaas at meduniwien.ac.at
>>>> ------------------------------------------------------------------------ 
>>>>
>>>>
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