[Chimera-users] perframe script

[Elaine Meng]

Hi Bala,
The distances all go to the Reply Log, you can save them from there.

See also these previous posts:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002379.html 
 >
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002378.html 
 >
(See link to python that can be used as a per-frame script at the  
bottom of that post.  In that case you would just define the distance  
monitor(s) by hand one time before running the script.  Again all of  
the info would go to the Reply Log, so it is basically similar to my  
Chimera per-frame script suggestion, except that you could modify the  
python to include frame number in the output lines.)

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 23, 2009, at 10:43 AM, Bala subramanian wrote:

> Hi Elaine,
> Your idea works. But how can direct the output to a file rather than  
> seeing it on the chimera window. I gave
> ~distance
> distance :163 at CA :166 at CA
> and then tried savefile option but nothing is saved in the output  
> file except the two lines of command. Could you please send me an  
> example script of doing some analysis on each frame of the  
> trajectory and just output to a file directly.
>
> Thanks,
> Bala
>
> On Wed, Dec 23, 2009 at 6:28 PM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> Hi Bala,
> Perhaps there is a more elegant way, but you could just add the  
> command ~dist to your per-frame script, i.e.:
>
>
> distance :163 at CA :166 at CA
> ~dist
>
> Of course, if the distance measurement is already present in  
> Chimera, also enter the command ~dist before starting to apply the  
> script so that the first time it runs, it will not generate that  
> error.  I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Dec 23, 2009, at 3:36 AM, Bala subramanian wrote:
>
> Friends,
> I loaded a amber trajectory in chimera. I simply want to calculate  
> the distance between two atom in each frame in the traj. and write  
> it to a text file. I used the per-frame utility in MD movie tool.
>
> I chose interpret script as 'chimera commands'
> substitute text 001-200 (frame 1 to 200)
>
> In the script section i gave
> distance :163 at CA :166 at CA
>
> It reports to me the following in the reply log.
> Distance between GLY 163 CA and ARG 166 CA: 5.083
> Problem in per-frame script:
> Distance monitor already exists
> Problem in per-frame script:
> Distance monitor already exists
> Problem in per-frame script:
> Distance monitor already exists
>
> How should i actually use the perframe option so that the analysis  
> will be done in each frame and reported output file will hve the  
> distance values for every frame.
> Thanks,
> Bala
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users