Normally it should be rendering double bonds by default, but you can change this setting in Preferences > Rendering > Structural models - check the Render multiple bonds option:
As for the PBT format, currently, SAMSON does not have the PBT format exporter, but you can export in OBJ or glTF formats for use in Blender.
There are several options for the colorization of structures or visual models (Ribbons is a visual model) based on chains:
The colorization using color schemes. First, select the Ribbons visual model in the Document view that you would like to colorize. Then:
Biology > Colorize > Chain ID or Chain (illustrative) (i.e. in the style of D.S.Goodsell)
You can also choose "Custom..." from the list and specify the color palette.
The colorization with constant colors per chain.
Choose a chain in the Document view.
Set the color using Visualization > Colorize.
In the new version, you can access the control parameters for the visual model via the Inspector. For that, simply select the Adenita visual model and open the Inspector - you can right-click on the Adenita visual model and choose Inspect in the context menu.
Hi Chris, thanks again for reaching out! As discussed, this was caused by having ligands with multiple connected components, which Vina cannot dock. We will try to provide clearer error messages to prevent this. Thanks again!
We have improved the performance of surface visual models (Gaussian, Solvent Accessible, and Solvent Excluded surfaces) in certain cases. For example, now animations with them should be much faster. The visual models should be automatically updated for you once you restart SAMSON.
we just released an update of the editors which makes it possible to use the current selection to build. This should make it easier to build any polymer you want by repeatedly adding larger and larger groups.
When using the Rectangle selection editor (the default editor, shortcut R), show the context menu (either by right-clicking in the viewport, right-clicking in the Document view, or clicking the green selection widget in the Document view). The third context menu action is Use selection to build:
Clicking this action automatically switches to the Add editor ands use the selection as a building fragment:
The Use selection to build action is also available in the context menu when the Add editor (shortcut A), Edit bonds editor (shortcut B) and Edit charges editor (shortcut C) are active. Here it is for example in the Add editor: