[Chimera-users] perframe script

Bala subramanian bala.biophysics at gmail.com
Wed Dec 23 10:43:38 PST 2009

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 :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.


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
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