[Chimera-users] Morphing a residue through MD trajectories

[Elaine Meng]

Hi Ken,
I thought George was asking about showing something as completely immobile (frozen) at the same time as the movements of some of the atoms in his trajectory.  That is what you could do with the separate PDB file. However, I could have misinterpreted the question.  Sometimes it is hard to guess what is going on! 

There is a “hold steady” option in MD Movie that tries to keep the (user-)specified atoms *within* the trajectory in the same place as much as possible. In that case, there will generally be slight movements as the relationships among even the specified atoms changes, but it should cut down on the large-scale movements of that group as a whole.  In that case you would not need a separate PDB file for anything.

The option is in the MD Movie menu: Actions… Hold selection steady.
Best,
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 8:38 AM, Kenward Vaughan <kay_jay at earthlink.net> wrote:

> 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
> here??)
> 
> 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?
> Chau!
> Kenward
> 
> 
>> 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
>>>>> 
>>> 
>>> 
>>> _______________________________________________ Chimera-users
>>> mailing list Chimera-users at cgl.ucsf.edu
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>>> 
>> 
>> 
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> 
> 
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