Learning how to manipulate and visualise protein structures
Demo Step 3: Getting familiar with ChimeraX
Below is a list of useful commands to manipulate your structure in ChimeraX. Try playing around with these functions (practice makes perfect!).
Mouse commands to manipulate structures
Move your structures around in the Working pane:
Left click + hold on the protein(s) to move it about on vertical & horizontal axis
Left click + hold on the background to rotate it about clockwise or anticlockwise along a fixed axis
Left click + Shift + hold to translate the protein
Scroll to zoom in & out
Select & deselect regions of your structure in the Working pane:
Left click + Ctrl + drag over an area of your protein to select this region
Left click + Crtl + click a specific residue to select a specific residue
Left click + Ctrl + Shift + an area/residue to add to or remove from the current selection depending if the area/residue is already in the selection or not
Left click + Crtl + click on the background to clear the current selection
Use Up/Down arrow keys to expand the current selection to the lower/higher resolution level (e.g. from a residue to the whole secondary structure it is contained in)
Note: to select at the atomic level (with your mouse), you will need to change the resolution of the protein representation first.
You can also define the function of your Right click through the Tool bar under the tab:
By default, the Right click is in Translate mode (green background = selected) but you can also change it to Zoom for example if you don’t have a Scroll button handy.
Click here for detailed information on the features in the tab.
In-line notation conventions – specifying models, chains and residues
There are conventions to specify or target structures and/or regions of interest in your commands. Different level notations are bricks that can be combined together.
For example: # followed by the model ID will specify the model. # alone selects all models loaded in ChimeraX. To specify several models, use the comma as separator (OR operator) e.g. #1,5 will select models 1 and 5. To select elements respecting 2 different conditions, use & (AND operator).
| Levels | Models | Chains | Residues | Atoms |
|---|---|---|---|---|
| Symbol | # | / | : | @ |
| Usage examples | #1 = model 1 #1,5 = model 1 & 5 |
/A = all chains A #1/A,B = chains A & B of model 1 only |
:1-25 = all residues with numbers 1 to 25 :tyr = all Tyrosines #1/A:1-25&:tyr = all Tyrosine residues with numbers between 1 and 25 and who belong to chain A of model 1 |
@ca = all C alpha atoms #1@ca = all C alpha atoms of model 1 |
The above course material is under CC-BY-SA license.