[chimerax-users] Question about using ChimeraX

[Elaine Meng]

Dear Lei Han,
ChimeraX does not show conformational changes of the protein if you only open one structure.

If you have multiple structures with different conformations, however, such as one for closed and one for open, then ChimeraX can create and display a morph movie open <--> closed  (or if more than two, like A, B, C in your figure, it can make a movie A -> B -> C).   There is a "morph" command to do it.  
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>

See this example which includes links to example command scripts:
<https://www.rbvi.ucsf.edu/chimerax/features.html#morphing>

...also the "making movies" tutorial:
<https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html>

...and structure analysis tutorial (last part):
<https://rbvi.github.io/chimera-tutorials/presentations/modules/chimerax-comp-structures/index.html#/>

However, if you only have one structure (open or closed) ChimeraX cannot automatically predict the other conformation.  You would need to build it manually somehow, or if you have the other conformation but for a different protein, by comparative modeling (Modeller).  Or, if the other protein has high sequence similarity with the other, another approach is to morph directly between the two different proteins if you only want to view the backbone (ribbons or cartoon but not sidechains).

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 17, 2023, at 12:27 AM, 韩磊 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Sir，
> 
> I hope this mail finds you well.  
> 
> I am a professional researcher from Tianjin Medical University, China. I have encountered some difficulties in learning to use ChimeraX software.
> 
> First, I would like to know if the software can be used to construct a graph of the process of channeling proteins from closed to open state (e.g., Appendix ). Second, we can currently only download and import a model of the closed state of a protein into the software, but it does not reflect its conformational changes, so I would like to know which option within the software can change the conformation of the protein.
> 
> Sincerely yours,
> 
> Lei Han, Ph.D.
> Tianjin Neurological Institute,
> Tianjin Medical University General Hospital,
> 154 Anshan Road, Heping District, Tianjin 300052, China
> 
> <20230417152045.png>