<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Dieter,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I guess next time look for "python" in the process table and also note its "state" column (titled "S"). You may not be able to kill the process if its state is "Z" (zombie process) or "U" (uninterruptible wait). Regardless, try to kill it with "kill -s KILL process_id".</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 15, 2020, at 12:56 PM, Dieter Blaas <<a href="mailto:dieter.blaas@meduniwien.ac.at" class="">dieter.blaas@meduniwien.ac.at</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
<div class=""><p class="">Dear Greg,</p><p class=""> as I stated, I moved the chimera windows to the bottom of
the screen and finally to another workspace. A day later, chimera
had closed. So I suspect that it is just a matter of time until it
closes.... Something seems to very much retard its reaction to
mouse clicks! I shall continue observing and use the 'Report a
Bug' if it occurs again....</p><p class="">thanks again, best, Dieter<br class="">
</p><p class=""><br class="">
</p>
<pre class="moz-signature" cols="72">------------------------------------------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at">dieter.blaas@meduniwien.ac.at</a>
------------------------------------------------------------------------</pre>
<div class="moz-cite-prefix">On 14.10.2020 08:12, Greg Couch wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:b091541d-1c6a-6ff7-8261-5e47f0fa023c@cgl.ucsf.edu" class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class=""><p class="">Chimera will show up as "python" in the process table. That's
one of the fixes we made with ChimeraX, it shows up as
ChimeraX. If you haven't done so already, when running Chimera,
please use the Help / Report a Bug... dialog so we have a record
of how your current system is configured (version of Linux,
graphics driver version, etc.). Are you still running Chimera
remotely using VirtualGL? If so, please state that in the
description.</p><p class=""> Thanks,<br class="">
</p><p class=""> Greg<br class="">
</p>
<div class="moz-cite-prefix">On 10/13/2020 10:46 PM, Dieter Blaas
wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:e3d68d00-b789-f786-e7de-a876f2965624@meduniwien.ac.at" class="">Hi,
<br class="">
<br class="">
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.... <br class="">
<br class="">
thanks for hints, bw Dieter <br class="">
<br class="">
------------------------------------------------------------------------
<br class="">
Dieter Blaas, <br class="">
Max Perutz Laboratories <br class="">
Medical University of Vienna, <br class="">
Inst. Med. Biochem., Vienna Biocenter (VBC), <br class="">
Dr. Bohr Gasse 9/3, <br class="">
A-1030 Vienna, Austria, <br class="">
Tel: 0043 1 4277 61630, <br class="">
Mobile: 0043 699 1942 1659 <br class="">
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true">dieter.blaas@meduniwien.ac.at</a> <br class="">
------------------------------------------------------------------------
<br class="">
<br class="">
On 06.10.2020 04:24, Dieter Blaas wrote: <br class="">
<blockquote type="cite" class="">Dear Tom and Eric, <br class="">
<br class="">
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. <br class="">
<br class="">
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! <br class="">
<br class="">
best, Dieter <br class="">
<br class="">
------------------------------------------------------------------------
<br class="">
Dieter Blaas, <br class="">
Max Perutz Laboratories <br class="">
Medical University of Vienna, <br class="">
Inst. Med. Biochem., Vienna Biocenter (VBC), <br class="">
Dr. Bohr Gasse 9/3, <br class="">
A-1030 Vienna, Austria, <br class="">
Tel: 0043 1 4277 61630, <br class="">
Mobile: 0043 699 1942 1659 <br class="">
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true">dieter.blaas@meduniwien.ac.at</a> <br class="">
------------------------------------------------------------------------
<br class="">
<br class="">
On 05.10.2020 20:58, Tom Goddard wrote: <br class="">
<blockquote type="cite" class="">Hi Dieter, <br class="">
<br class="">
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. <br class="">
<br class="">
Maybe you are on Linux or maybe Chimera is hung on some
web service you are using like BLAST.... <br class="">
<br class="">
Tom <br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Oct 5, 2020, at 11:30 AM, Eric
Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu" moz-do-not-send="true"><pett@cgl.ucsf.edu></a>
wrote: <br class="">
<br class="">
Hi Dieter, <br class="">
Instead of "kill process_id" try "kill -s KILL
process_id". <br class="">
<br class="">
--Eric <br class="">
<br class="">
Eric Pettersen <br class="">
UCSF Computer Graphics Lab <br class="">
<br class="">
<blockquote type="cite" class="">On Oct 4, 2020, at 9:05 AM, Dieter
Blaas <a class="moz-txt-link-rfc2396E" href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true"><dieter.blaas@meduniwien.ac.at></a>
wrote: <br class="">
<br class="">
Hi, <br class="">
<br class="">
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? <br class="">
<br class="">
Thanks for hints, best, Dieter <br class="">
<br class="">
-----------------------------------------------------------------------
<br class="">
Dieter Blaas, <br class="">
Max Perutz Labortories <br class="">
Medical University of Vienna, <br class="">
Inst. Med. Biochem., Vienna Biocenter (VBC), <br class="">
Dr. Bohr Gasse 9/3, <br class="">
A-1030 Vienna, Austria, <br class="">
Tel: 0043 1 4277 61630, <br class="">
Mobile: 0043 699 1942 1659 <br class="">
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:dieter.blaas@meduniwien.ac.at" moz-do-not-send="true">dieter.blaas@meduniwien.ac.at</a>
<br class="">
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