[Chimera-users] Morphing a residue through MD trajectories

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 1 07:58:26 PDT 2015

Hi George,
You can hide whatever parts of the trajectory structure you want, just like for other structures in Chimera.  So even if the trajectory includes a protein receptor plus ligand, you could hide the protein ribbons/atoms and only show the ligand during playback.  For your frozen receptor, you can have another PDB file opened the regular way (directly in Chimera, not as a trajectory) at the same time; just keep it displayed while you are playing back the trajectory.

On Aug 1, 2015, at 7:52 AM, George Tzotzos <gtzotzos at me.com> wrote:

> Thank you Elaine,
> I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest.
> Have a good day
> George
>> On 1 Aug 2015, at 17:46, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi George,
>> I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations.  As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
>> Maybe you want to play back this trajectory as a time series.  In that case you need to open it in the MD Movie tool (the trajectory viewer).  If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory.  First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis).  A dialog will appear requesting the input trajectory file(s).  You should change to the proper format setting and then browse to your file location in that dialog.   Then your trajectory will be open as a trajectory.
>> You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest.  With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
>> MD Movie documentation:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
>> See also the Trajectory and Ensemble Analysis tutorial:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
>> 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 Aug 1, 2015, at 7:25 AM, George Tzotzos <gtzotzos at me.com> wrote:
>>> Hi,
>>> I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better.
>>> I’ve tried to follow the instructions but obviously, I get it wrong.
>>> I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. 
>>> Any help would be most welcome
>>> Regards
>>> George
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