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

Marek Maly marek.maly at ujep.cz
Sat Jun 1 10:48:42 PDT 2013

Thanks Elaine !

it works perfectly,

   Best wishes,


Dne Sat, 01 Jun 2013 18:40:41 +0200 Elaine Meng <meng at cgl.ucsf.edu>  

> 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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