[Chimera-users] Motion of an atom

[Conrad Huang]

This script works for me on the current daily build.  It should work on 
all versions of Chimera.

Conrad

On 7/11/12 6:26 AM, Raju Purohit wrote:
> wait function doesn't seem to help. If I use wait(<some positive
> integer>), python stops executing ahead and hangs. If I use wait(<zero
> or some negative integer>), the code runs ignoring wait.
>
> This is my program:
> I have defined a variable atom1 which is an atom in chimera. Then I
> execute this program:
>
>  >>> atom1.setCoord(chimera.Point(0,0,0));
>  >>> for i in range(5):
>       time.sleep(0.1);
>       atom1.setCoord(chimera.Point(0,0,i));
>       wait(1);
>
> I was expecting to see the atom move by 1 unit every loop but that does
> not happen. What would you suggest me to insert in this for loop so that
> the value on atom1 is updated in chimera?
>
> Thank you.
>
> On Tue, Jul 10, 2012 at 7:22 PM, Eric Pettersen <pett at cgl.ucsf.edu
> <mailto:pett at cgl.ucsf.edu>> wrote:
>
>     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
>     wait(1)
>
>     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
>
>                              Eric Pettersen
>                              UCSF Computer Graphics Lab
>     http://www.cgl.ucsf.edu
>
>     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
>>
>>     _______________________________________________
>>     Chimera-users mailing list
>>     Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>     http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
>
>
> --
> 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
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

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