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Cryo-EM ​

The Cryo-EM plugin allows you to load Cryo-EM maps into Nanome.

There are two ways to load a map into Nanome

  1. Load a map from the Electron Microscopy Data Bank (EMDB), and align it with it's corresponding model from RCSB database.

  2. Load Maps and models from your Vault.

Instructions ​

Load Map and Model ​

Cryo-EM main menu

  1. Ensure that a MapGroup is selected on the right hand side of the main menu

    • Map groups are used to organize your maps and models. You can have 1 map per Mapgroup, with multiple models.
    • The map group with a green square next to it is the one that the maps/models will be added to in the following steps

  2. Select which method you wish to load the map with

    Load from Vault ​

    • The Browse Vault button will open the Vault navigation menu.
    • Find the maps and models you have already uploaded, select them, and press Load.

    Load from EMDB ​

    Load from EMDB Menu

    Find the EMDB ID for the map you wish to load. Enter the id in the Textbox and press Load

    • The Browse EMDB button will open EMDB in the web browser
    • Files must be under 500MB. Unfortunately there is no way to tell unless you try loading it.
    • After the Map loads, the RCSB code will be prepopulated in the next Textbox. Load this by pressing load.
    • The structure will be added to your workspace, and aligned to the previously loaded map.

Edit Map ​

Cryo-EM Edit Map Menu

To edit map colors and isovalues, click the mapgroup on the right hand side. This will open the Edit Map Menu.

Edit Isovalue ​

Select a new isovalue on the slider, and press the "Redraw Map" button

Change Color Scheme ​

On the bottom of the menu, there is a dropdown to edit the coloring scheme of the map.

Note that color schemes are based on loaded model, so just a map on its own will not be colored.

Color Options:

  • Element: When a model is present, the map is colored according to the nearest element on the model
  • BFactor: Colored according to model BFactor
  • Chain: Each chain on the model is given a different color.

Map Boxing Options ​

We provide the ability to only show a subset of the loaded map.

There are 3 ways to edit the section of the map rendered.

  1. Show Full Map: This will render the entire map. This is the default load mode, so its useful for resetting after using other boxing methods.
  2. Box Around Model: When a model has been added to the Mapgroup, this will only render the map around the model.
  3. Box Around Selection: The map will be rendered around selected atoms on the model. This is useful around larger models, when you only want to see a small subset.