[chimerax-users] Molecular Dynamics Viewer

[Elaine Meng]

Hi!
Some steps would have to be done in Chimera, so you might rather use Chimera.  However, if you really want to render in ChimeraX, it may be doable by using both programs, as detailed below.

(1) We would need an example file to be able to say or do anything about this.  Sounds like the bonds are missing, but I don’t know what formatting issue would allow them to be shown in Chimera but not ChimeraX.  You could use ChimeraX menu: Help… Report a Bug and attach the file plus short description and your e-mail address if you want feedback.

(2) If the PDB with the B-factors you want has EXACTLY the same atom/residue/chain names as the trajectory PDB files, I imagine the following:
 
(a) in Chimera, open the PDB file with the B-factors.  Use Render by Attribute tool (Tools… Structure Analysis... Render by Attribute) menu: "File… Save Attributes” to save atomic attribute named bfactor to an assignment file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

(b) still in Chimera, close that PDB and using MD Movie (in menu under Tools.. MD/Ensemble Analysis) open the trajectory from multiple PDB files  and then assign the bfactor values from the file using Define Attribute tool (Tools… Structure Analysis… Define Attribute) or “defattr” command.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html>

(c) still in Chimera, save the whole trajectory as a multi-model single PDB file.  (ChimeraX cannot open a trajectory from multiple PDB files.  If you can’t make it a single file, then you would need to use Chimera.)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>

(d) in ChimeraX, open the trajectory and color by bfactor however you like, e.g. commands:

open my-multimodel-trajectory.pdb coordset true
color byattribute bfactor palette rainbow range 2,100

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>

(e) in ChimeraX, show the trajectory with the slider graphical interface or “coordset” command. 

In the future more of these steps could be done in ChimeraX, but for now, you’d need to use a combination of the two programs.

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

> On Jul 11, 2019, at 1:48 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Dear ChimeraX users!
> 
> I would like to make a movie of molecular dynamics trajectory that has
> been pre-converted to pdb format (totally 250 frames).
> 
> 1) Firstly, I have a problem with the recognition of the SS elements
> of that ensemble in ChimeraX, where each snapshot looks just like a
> mixture of points ( i tried to use dssp but it did not solve the
> issue). At the same time the snapshots looks fine in another viewers
> including UCSF Chimera (not X)
> 
> 2) If I have a pdb of the same protein with mapped B-factors and then
> I colored it using
> color byattribute bfactor palette rainbow range 2,100
> 
> 2) would it be possible to map the trajectory to that pdb in order to
> see the motions (observed in MD) mapped onto the structure that has
> been coloured by b-factors?
> 
> Thanks for help!