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Hi,

I would like to extend the assembly example to allow for assemblies across different PDB IDs (essentially, have a select box with a custom list of PDBs for filtering). From what I can tell the software seems to support such cases (perhaps using EntryAssembliesCollector?), but since I am only superficially familiar with TypeScript I don't know how I would go about implementing this.

Perhaps I have to use the RcsbFv3DCustom class for this, instead? I'd appreciate a few pointers in terms of what direction to take.

Hello, I'm in a team that's trying to use your saguaro-3d app to display papillomavirus protein structures along with some pairwise alignments and other associated data. We found this project when researching how to integrate molstar into our project, and it seems like you've already done a lot of the legwork, thank you so much.

I had a question about how to update the sequence panel block config after the initial object instantiation. We are using saguaro-3d as in your cdn-examples currently.

When I call the updateConfig function, I can change the sequence panel's title and subtitle, but not its blockConfig (for example to change the alignment shown, remove an Axis, change a color, etc.).

I made a jsfiddle with the single-chain example config, and a button with a handler that attempts to change the config. I assume it's something in the structure of the config I'm passing, but it seems like this conforms to the documentation.

What am I doing wrong?

Thanks again for all your great work.

Hi,
I have a custom extension (with labeling and color theme).
How do I get rcsb-molstar to use this extension?

I attempted RcsbFv3DCustom constructor, but it can expect
built-in mol* extension names here, as I see:

params.structureConfig.structureViewerConfig.viewerProps.extensions:

("rcsb-assembly-symmetry" | "rcsb-validation-report" | "rscc" | "anvil-membrane-orientation" | "ma-quality-assessment" | "model-export" | "mp4-export" | "geo-export")[]

Furthermore, I guess, I should register the extension by the embedded PluginContext,
but I can't see any property to access underlying mol* viewer instance.

Best regards,
Csongor

Hi @bioinsilico, continuing from before:

Is there a way to specify the sequence loaded into the molstar sequence panel (for example by labelAsymId) on startup?

I saw that there was a params and a props that seem to pass values to the molstar init, but I don't see any options that might relate to setting the initial state (e.g. chain, entity, etc) on the sequence pane.

Do you have any advice?

Thanks for your help

I complete the rendering of the page through RcsbFv3D.assembly, and get the chain collection through onChangeCallback. Now I want to switch chain[A,B,C,D] through code. can you tell me how to do

It looks like the example files under /cdn-examples may be out-of-date with the latest CDN release. When I attempt to run the single-chain example I receive a pair of errors. One is related to the Mol* interface's loadParams. It looks like pdbId has been changed to entryId: https://rcsb.github.io/rcsb-saguaro-3d/interfaces/RcsbFv3DAssembly._internal_.LoadParams.html.

var molstarConfig = {
loadConfig: {
loadMethod: "loadPdbIds",
loadParams: [{
pdbId: "1ash",
id: "1ash_model"
}]
},

needs to be:

var molstarConfig = {
loadConfig: {
loadMethod: "loadPdbIds",
loadParams: [{
entryId: "1ash",
id: "1ash_model"
}]
},

The other error appears to be related to the RcsbFvSelectorManager: RcsbFvSelectorManager. It looks like an additional layer has been added to the object, so that index.js lines 90-91 need to be updated:

current:
structureSelectionCallback: function (plugin, pfv, selection) {
var sel = selection.getSelectionWithCondition("1ash_model", "A", "select");
should be:
structureSelectionCallback: function (plugin, pfv, selection) {
var sel = selection.selectionState.getSelectionWithCondition("1ash_model", "A", "select");

I believe there are likely other errors related to the RcsbFvSelectorManager elsewhere in the file as well. It would be extremely helpful to have these two example files working, since they've been useful references in the past.

There is a browser back call during the RcsbFV3DCustom.unmount call. Is there any way this could be optional?