representation size?

[Glucksistemi]

I have a structure with molecule in a water box. If I set 'ball_and-stick' representation to water, i get something like this:

In Mol* itself I can set size of representation items (see figure below) but I found no option to control it from MVS.

So, is there a way to control such aspects of visualisation from MVS structure?

[sbittrich]

Hi @Glucksistemi,

That's not possible at the moment. MolViewSpec only supports a small subset of the options available in Mol*. However, we are adding more detailed parameters as we go. Size (and transparency/opacity) are good candidates for that.

[Glucksistemi]

@JonStargaryen, thank you for reply! I already found that it's not possible, but I hope that case I explained in this topic will help you with priorities for further development of MVS

[Raiyan-Rizwan]

Hi,
I wanted to ask if the feature to resize representations was added to MolViewSpec. It would be really helpful for me if it was available.

Thanks

[sbittrich]

Hi @Raiyan-Rizwan,

Not yet available but scheduled to be added soon. Thank you for your patience.

[Raiyan-Rizwan]

Ok no worries. However, I was having issues visualizing protein structures with their respective cluster files(which represent the binding sites). However, each time I create the builder, get its state, upload it to Amazon AWS, and launch an HTML file to view it, the visualization page pops up on google, and keeps on loading until the browser crashes. I face this issue with files larger than 600 kilobytes. The problem is that majority of my cluster files are atleast 1,000 kilobytes, and I need to visualize each cluster file separately alongside their respective protein structures. Here is a sample cluster file I use. Let me know if you can provide me with a solution to this issue.

6YAC_1_cluster_1.zip

Just for your reference, if it helps you suggest me solutions, the cluster files which do load look like this: And this is what I am aiming for with the other files.

[dsehnal]

I think instead of this, it might make more sense to use the upcoming geometrical primitives. This is a Mol* issue -- Mol* is not well equipped to render such small structures with 23k chains, one atom each... essentially the structure representation algorithm goes haywire.

But I think the MVS primitives (once fully available, for now you would have to construct the mesh manually) should be able to handles rendering this many spheres quite easily.