[Chimera-users] Morphing a residue through MD trajectories

Kenward Vaughan kay_jay at earthlink.net
Sat Aug 1 08:38:07 PDT 2015

On 08/01/2015 07:58 AM, Elaine Meng wrote:
> 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. Elaine

Hi Elaine,

Following up on this myself with a question...  As George was describing
things I found myself wondering if what you were suggesting actually
accomplishes what *I* was visualizing?  (Interesting 3-way conversation

Things bounce around during a trajectory.  Can the various steps be auto
rotated/oriented/scaled so that the ligand does not appear to move from
one frame to another?

Is this what is accomplished by having the other file opened?



> 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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