The Cryo-EM plugin allows you to load Cryo-EM maps into Nanome.
There are two ways to load a map into Nanome
Load a map from the Electron Microscopy Data Bank (EMDB), and align it with it's corresponding model from RCSB database.
Load Maps and models from your Vault.
# Load Map and Model
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
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 EMDBLoad 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
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.
- 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.
- 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.
- Box Around Model: When a model has been added to the Mapgroup, this will only render the map around the model.
- 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.