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 use 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.