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LocScale-SURFER in ChimeraX

LocScale-SURFER provides a GUI in ChimeraX from which all map operations can be performed.

Step-by-step tutorial

In this example we will use the pentameric calcium-sensitive channel DeCLIC from Desulfofustis glycolicus reconstituted in lipid nanodiscs 1. You can download the maps here: EMD-19995

  • Start ChimeraX session


    SURFER_tutorial_01 Start up ChimeraX and load unsharpened map, LocScale-FEM (feature-enhanced) map and FDR confidence mask.

  • Launch LocScale-SURFER


    SURFER_tutorial_02 LocScale-SURFER is located under the Volume Tools menu. This will launch the GUI.

  • Start micelle/membrane prediction


    SURFER_tutorial_03 In the LocScale-SURFER GUI select the raw, unsharpened map and the FDR confidence mask from the LocScale run. If you do not have an FDR mask you can generate one on the fly (in this case leave the mask field empty). Then press "Segment". This will take 1-5 min, depending on the size of your map.

  • Segment and subtract micelle/membrane


    SURFER_tutorial_04 Select the map from which the segmented micelle should be subtracted (in this case the feature-enhanced map from LocScale-FEM) and choose a removal threshold (this is the threshold of the removal mask - called "predicted_micelle"). Typically the 0.5 default is fine, but you may have to tune it. The mask should cover your detergent belt/micelle/nanodisk without cutting into remaining density. "Remove" will then create a new volume with the micelle substracted.

  • Toggle between maps with and without micelle


    SURFER_tutorial_05 You can toggle between both maps with the toggle switch in the LocScale-SURFER GUI. Here contextual information is OFF.

  • Toggle between maps with and without micelle


    SURFER_tutorial_06 You can toggle between both maps with the toggle switch in the LocScale-SURFER GUI. Here contextual information is ON.