[Chimera-users] Showing/Hiding/Fading

[Gustaf Olsson]

Hello Chimera users and developers, I’m back again.

So my movie rendering is progressing though I have of course run into more problems. I have one PDB file open, I need to create a surface around one molecule that is close to other molecules so running the surface command directly does not work as intended. I therefore have to split the PDB file and calculate a surface around a single molecule. All is well, however after this I run into some problems trying to clean up the script. I assume that I am defining the modelID incorrectly though I cannot figure out how.

The following works:

    split #0 atoms :17.het
    surface probeRadius 0.5 vertexDensity 20.0 :17.het
    coulombic -5 red 0 white 5 blue :17.het
    wait
    combine #0.1-2 modelId 0 close true
    surftransparency 100 #0.1

This splits the model putting one residue (17) in a separate model, I calculate the surface without issue, color it by coulombic charges. I then have to combine the models (the single residue (17) and the rest of the residues) and close the old “residue 17” model. I then need to hide the newly created surface to display it at a later point in the movie. The script above works, however this does not seem very neat.

I have experimented with different other commands, including transparency

    transp 100,s #0.1

Which also works well, as long as I split and combined the models. However, I have to combine the model for this to work!

    split #0 atoms :17.het
    surface probeRadius 0.5 vertexDensity 20.0 :17.het
    coulombic -5 red 0 white 5 blue :17.het
    wait
    combine #0.1-2 modelId 0 close true
    surftransparency 100 #0.1

Everything but hiding the surface works.

    transp 100,s #0.1

This does not work either in this case. I am assuming that I am not defining the model ID correctly for the surface and this is why I cannot hide it? I also tried using surfcat:

    surfcat templ :17.het
    surf probeRadius 0.5 vertexDensity 20.0 templ
    coulombic -5 red 0 white 5 blue templ
    wait
    surftransparency 100 templ 

or any of the following:

    surftransparency 100 #0
    surftransparency 100 :17.het
    surftransparency 100 #0:17.het
    transp 100,s #0

Hides the created surface, what am I doing wrong in defining the surface to hide it and show it again?

Thank you for any input and best regards
// Gustaf