[chimerax-users] Molecular Dynamics Viewer

[James Starlight]

Thank you so much, Elaine!
Yes, indeed, it was a problem with rendering of residues according to
their attributes of the averaged bfactors. I am going to look how to
do it in Chimera ..

J

пт, 12 июл. 2019 г. в 18:17, Elaine Meng <meng at cgl.ucsf.edu>:
>
> Hi James,
> We haven’t implemented trajectory smoothing.  ChimeraX doesn’t have much trajectory analysis yet, as mentioned in the “missing features” on the download page.  The trajectory input types besides single PDB file are listed in the input formats table:
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
>
> It works a little differently than in Chimera.  For these condensed trajectory formats you also have to open another file (which could be a single PDB structure) to provide the topology.  See link above for details.
>
> There is a ChimeraX plugin that you can download from the Toolshed (ChimeraX menu Tools… More Tools..) named MolecularDynamicsViewer but I don’t know in detail what it does, other than show the trajectory opened from a multimodel PDB file.  It has a graphical interface. You could see if it makes what you’re doing any easier.
>
> For your previous questions about Chimera:
> the defattr command just opens your attribute file exactly the same as using the Define Attribute tool.  I don’t know for sure what is wrong with your using the Render dialog instead of rangecolor command, but probably you are not displaying the atoms but ribbons.  To color ribbons, you have to render by residue (not atom) attribute, average bfactor.  (the Chimera rangecolor command automatically does that, coloring atoms by the atomic values and coloring ribbons by the residue values)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jul 12, 2019, at 8:14 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> >
> > some additional (more general) questions about MD trajectory analysis
> > with Chimera and ChimeraX
> >
> > 1- is it possible to set some kind of smoothing on the trajectory
> > (based on the analogy with v*d - trajectory smoothing windows size) ?
> >
> > 2- does Chimera-X recognize any other formats for trajectories besides
> > pdb (in the same manner like it does Chimera)?
> >
> > thanks in advance !
> >
> > пт, 12 июл. 2019 г. в 11:49, James Starlight <jmsstarlight at gmail.com>:
> >>
> >> Hi Elaine,
> >>
> >> Thank you so much for your suggestions! It seems to me that it works
> >> great but presently I am stacking on the step D.
> >>
> >> Probably I have created the attribute file in a wrong way, because
> >> normally in Chimera I can colour b-factors using
> >> rangecolor bfactor key 1 blue 300 yellow 500 red   , which works fine
> >> with my B-factor file.
> >>
> >> Now, then I try to do the same using GUI window of Render/Select by
> >> Attribute (in which I can also save the attribute file, which is gonna
> >> to mapped onto the trajectory on the next step), nothing happens with
> >> the coloring of atoms while clicking Apply or Done ( I select
> >> attribute bfactor, color atoms, setting the attribute to atoms) ...
> >>
> >> M.b. in my case it would be better to use "defattr" indeed in the same
> >> manner how I did it via "rangecolor bfactor" ?
> >>
> >> thank you in advane!
> >>
> >> James
> >>
> >> чт, 11 июл. 2019 г. в 19:51, Elaine Meng <meng at cgl.ucsf.edu>:
> >>>
> >>> 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!
> >>>
> >
>