EMalign is an algorithm for aligning maps with respect to rotation, reflection, and translation.
This bundle is deigned to be installed as a plugin to ChimeraX.
Note that the algorithm is aimed to align two maps of the same structure (for example, two half maps), and not to fit a small structure into a larger one. The two maps can have different dimensions and pixel size, but should represent similar structures.
You can also install the plugin through the ChimeraX toolshed at https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxemalign
- Download the emalign4chimerax folder and save it in the designated directory (PATH=emalign4chimerax folder).
- Open ChimeraX and run the following commands in the command line bar at the bottom of the screen:
devel build PATH\emalign
devel install PATH\emalign
devel clean PATH\emalign
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Restart ChimeraX, then the EMalign tool should appear in the toolbar:
Open ChimeraX and navigate to the 'Volume' menu. Select the EMalign tool from the list.
- Selecting maps:
In the EMalign tool window, select the reference map and the query map from the dropdown menus.
- Setting alignment parameters:
Set the parameters for alignment, such as rotation, translation, and reflection options.
Adjust these settings as needed for your specific use case.
- Running the alignment:
Click the 'Align' button to start the alignment process.
The tool will automatically handle the alignment and provide a progress log when finished.
- Viewing the aligned maps:
Once the alignment is complete, you can view the aligned maps directly in ChimeraX.
The aligned maps will be displayed, and you can further analyze or manipulate them as needed.
