[Chimera-users] perframe script

[Elaine Meng]

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