[Chimera-users] How to force Chimera to properly analyze and visualize in each MD movie frame the ribon representation of the protein structure ?

Elaine Meng meng at cgl.ucsf.edu
Sat Jun 1 09:40:41 PDT 2013


Hi Marek,
Yes, we recommend that for ribbon display of protein trajectories, you re-evaluate the secondary structure at each frame.  This can be done fairly easily in MD Movie with a per-frame Chimera command script.  In the MD Movie menu, choose Per-Frame... Define Script, use Chimera commands (as opposed to Python), and enter the script, which could just be:

ksdssp

OK/Apply will start running that script at each frame.

MD Movie documentation:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

The need to re-evaluate secondary structure is mentioned in the "viewing frames" section, and there is also a section about per-frame scripts.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#viewing>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

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 Jun 1, 2013, at 8:18 AM, Marek Maly wrote:

> Dear all,
> I just found that if one loads several frames from the simulation
> (Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character
> of ribons (random colil, beta sheet, alpha helix) just using the first
> loaded frame and even if structure of the protein is changing in the
> next frames (e.g. forming beta sheet structure from the originally random coil),
> the visual ribon representation is not changed.
> 
> I found this, when I loaded just the isolated frame from the simulation and
> saw nice forming of the local beta sheet which was nicely highlighted by
> proper ribon representation (wide arrow) in the palce where was originally (in the initial frame) just random coil. But when I loaded both (initial frame and that after some MD simulation),
> chimera keep to use random coil representation for both frames.
> 
> I did also reverse experiment i.e. first loaded later frame from MD simulation and
> then the initial frame and this time chimera fixed for both frames beta sheet representation
> in that protein area. Please is there any possibility to prevent such unwanted behavior and
> to force Chimera that analyses properly protein configuration at each loaded frame and eventually
> changes properly the ribon representation ?
> 
>    Thank you in advance for any useful advices !
> 
>        Best wishes,
> 
>           Marek




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