[Chimera-users] Terminating Match-align without loosing reply log

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 27 12:16:01 PDT 2009

Hi Mario,
	There is no guaranteed way.  On the Mac or on Linux you may be able  
to stop the computation by sending Chimera's Python interpreter an INT  
signal (terminal interrupt) [I don't know of any such option on  
Windows].  Open a terminal window (on Mac: /Applications/Utilities/ 
Terminal.app).  Find Chimera's Python process via:

ps augxww | grep python

You'll see something along the lines of:

pett     86576  98.7 13.4  1218088 562256   ??  R    11:58AM    
2:17.97 /Users/pett/Applications/Chimera-daily-x11.app/Contents/ 
Resources/bin/python2.5 /Users/pett/Applications/Chimera-daily-x11.app/ 

The first number (86576) is the process ID of Chimera's Python  
interpreter.  Send it an interrupt signal by:

kill -INT 86576

If all goes well, Chimera will bring up an error dialog saying  
something about KeyboardInterrupt.  The Match->Align computation will  
have stopped with the structures in the same position as they were at  
the end of the last iteration, the last alignment window will be up,  
and the Reply Log will be available.

On Linux, if you started Chimera yourself from the command line you  
may be able to just hit control-C (or whatever your interrupt  
character is) instead of the rigamarole above.


On Oct 27, 2009, at 11:46 AM, Mario Borgnia wrote:

> Hi Eric,
> Thanks for the fast response. My other question is how to terminate  
> the process
> in progress without compromising the output of previous iterations.  
> Thanks!!!
> Mario
> Eric Pettersen wrote:
>> Hi Mario,
>> The iterations are independent.  So you could iterate twice, save a
>> session, and then iterate further later.  You could use the 'Save'
>> button on the Reply Log to save info as needed.
>> --Eric
>> P.S.  Sorry it's slow.  It's all in Python and given how complex it  
>> is
>> it's unlikely it's going to be recoded in C++ anytime soon.
>>                        Eric Pettersen
>>                        UCSF Computer Graphics Lab
>>                        http://www.cgl.ucsf.edu
>> On Oct 27, 2009, at 7:47 AM, Mario Borgnia wrote:
>>> Hi,
>>> I launched a massive match-align procedure with five iterations
>>> without knowing
>>> that it would take so long to complete. Is it possible to stop it at
>>> iteration 2
>>> without loosing the information computed to that point? Also, is it
>>> possible to
>>> continue from that point on in a subsequent round?
>>> Thanks!
>>> Mario

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