[Chimera-users] Motion of an atom

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 10 10:22:01 PDT 2012

Hi Raju,
	During the execution of a Python script, Chimera does not redraw the graphics screen until explicitly requested or when the script ends.  The simplest way to ask for a redraw is to execute the "wait 1" Chimera command, which you can do from Python with:

from chimera import runCommand
runCommand("wait 1")

So if you embed that in your loop you should be able to see your atom move.  Frames are redrawn at a rate of 25 per second (though future versions of Chimera may allow faster redraw rates), so you may want to wait more than 1 frame if the atoms moves too fast.
	Alternatively, there is also a direct Python call to wait():

from Midas import wait

	FYI, there is another mailing list, chimera-dev, where programming-intensive questions like this one are more appropriate, so that the regular user's eyes don't glaze over. :-)


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Jul 10, 2012, at 9:07 AM, Raju Purohit wrote:

> Hello friends,
> I need some help here.
> I created a basic model having just an atom and set its coordinates as (0,0,0). Now I want to make it move along a certain path defined mathematically (say, along x axis) and I need to see it move. So I used a for loop. But I couldn't see and motion and soon realised that the loop is very quick in executing and thus I could see the atom at its last coordinates. So I tried to add delay of 0.5 seconds for each loop by importing time module and useing time.sleep. But still I couldn't see any motion and the coordinates of the atom is set only at the end of the for loop. I could not see the intermediate path. I am sure you people must have tried this earlier and this problem has a solution but I just couldn't figure it out. 
> Can you please help me out?
> Thank you in advance.
> -- 
> Raju R.N.
> Third Year, B.Tech
> Mechanical Engineering
> National Institute of Technology Karnataka, Surathkal
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> Chimera-users at cgl.ucsf.edu
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