[chimerax-users] movie in ChimeraX

[Elaine Meng]

As I said in the previous message, the example where the ligand is moving is in the Chimera movie-making tutorial, except that in ChimeraX you would use "view" command instead of "savepos" and "reset".  See the section with heading "Ligand flying into unbound conformation":

> You can show ligands but because they are not included in the morph model, you have to display the ligand(s) from the original model (or an additional copy of the original model) along with the protein in the morph model.  Moving them to different positions is even more complicated than showing/hiding.  There is a Chimera tutorial that covers this, and what you would do with ChimeraX is similar except that ChimeraX "view" is used to save and restore positions instead of the Chimera commands "savepos" and "reset":
> <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html>

Elaine

> On Mar 24, 2021, at 4:05 AM, Ruchika Bajaj <phd.ruchika at gmail.com> wrote:
> 
> Hi Elaine
> Thanks for sharing the following link for chimeraX movie. I followed the tutorial well. I see that the ligand in this movie is static, i.e. the position of the ligand didn't change while different frames of morph are moving. However, I am trying to make a movie in which the position of the ligand needs to change while it moves. Can you please direct me towards right commands. 
> Thanks !!
> Regards
> Ruchika  
> 
> On Tue, Mar 23, 2021 at 8:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> See also the ChimeraX morphing example in the feature highlights, including the linked ".cxc" files (ChimeraX command scripts):
> 
> <https://www.rbvi.ucsf.edu/chimerax/features.html#morphing>
> 
> > On Mar 23, 2021, at 7:48 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 
> > 
> > 
> >> On Mar 23, 2021, at 5:04 AM, Ruchika Bajaj <phd.ruchika at gmail.com> wrote:
> >> 
> >> Hi Elaine 
> >> I am trying to figure out two things. Could you please help me with this? I would appreciate your help. 
> >> 1. I have two structures. The first one doesn't have a ligand and the second one has two ligands. I am trying to make a movie with these steps. 1) first structure, 2) two ligands are coming or flying in the picture, 3) then the 2nd structure with two ligands. However, when I am trying to make the morph between the first and second structure, it doesn't show any ligand. I did check the following link, where it discusses that both structures should have ligands to include it in the morph. So, my question is how should I include the ligand ? Could you please explain me with command usage? Thanks !! 
> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> >> 2. I heard that frames/sec rate could be increased to smoothen steps in movies. I checked the maxFrameRate command. However, I don't know the usage. Could you please help me with that ? 
> >> Thanks a lot for your help !! Your prompt response would help me to proceed further. 
> >> Regards
> >> Ruchika
> > 
> > Hi Ruchika,
> > Please send questions to chimerax-users at cgl.ucsf.edu (if you are using ChimeraX) or chimera-users at cgl.ucsf.edu (if using Chimera) rather than my individual address, or else they may not get answered.
> > 
> > (1) as explained here
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> > morph only contains the atoms that are the same in both start and end structures.  You can show ligands but because they are not included in the morph model, you have to display the ligand(s) from the original model (or an additional copy of the original model) along with the protein in the morph model.  Moving them to different positions is even more complicated than showing/hiding.  There is a Chimera tutorial that covers this, and what you would do with ChimeraX is similar except that ChimeraX "view" is used to save and restore positions instead of the Chimera commands "savepos" and "reset":
> > <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html>
> > 
> > (2) if you mean you want more steps in the morph (more gradual change) then you would use the "frames" option in the morph command.  Probably that is what you want.
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#top>
> > 
> > However, if you really mean you wanted movie framerate, then it is the "framerate" option of the "movie encode" command.
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode>
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                       
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > 
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