Visualizing Small-Molecule Density in Crystal Structures with ChimeraX

Intro

You will need:

1. ChimeraX installed
2. A PDB file containing the crystal structure coordinates
3. An MTZ file with the electron density corresponding to the PDB file

This post uses 7VH8 as an example. Follow this article to get the PDB and MTZ files.

TL;DR

1. Open ChimeraX and install Clipper. There are two ways to install it:

   1. In the GUI, go to Tools -> More Tools... and install it from there.
   2. Run the command toolshed install clipper.

2. After opening the PDB file, drag the MTZ file into the window. A dialog will pop up; select the corresponding PDB.

   

   Once opened, it should look like this:

   

3. Display the density:

   1. First, let's change the background color to white:

      CHIMERAXCopy

      set bgcolor white
      

   2. Then select the small molecule:

      CHIMERAXCopy

      sel #1.2:4WI
      

   3. Display only the density around the small molecule:

      CHIMERAXCopy

      clipper isolate sel surroundDistance 0 contextDistance 5 maskRadius 2.5 hideSurrounds true focus true
      

      Parameter	Description
      sel	Refers to the currently selected atoms (i.e., the small molecule)
      surroundDistance	Specifies how far to extend the selection; the default is 0 Å. This parameter determines which atoms, in addition to the selected ones, are included when computing the region covered by the map.
      contextDistance	Sets the distance of the additional context region to display; the default is 5 Å. These atoms are shown but not covered by the map.
      maskRadius	Specifies the radius of the map mask; the default is 3 Å. This determines how far the map extends around the selected region.
      hideSurrounds	If true, atoms outside the surroundDistance range are hidden (cartoon display is not affected)
      focus	If true, the view resets and centers on the covered region

      

   4. Adjust the contour level and assign a color:

      Note that Coot and ChimeraX use different conventions for the contour level:

      Software	Contour Level
      Coot	By default, contour levels are expressed in standard deviation (sigma) units (although the software displays them as RMSD). When the contour level is set to 1.0 in Coot, it actually means that regions with density values greater than or equal to the mean density plus 1.0 standard deviation are displayed.
      ChimeraX	The contour level is usually expressed as an absolute electron density value (electron/ų). When you run the command volume #1 level 1.0, it displays regions with density values equal to or greater than 1.0 electron/ų.

      Therefore:

      • If you want to set the contour level in standard deviation units in ChimeraX, use sdLevel, which is the same concept as in Coot.

      • If you want to set the contour level in root-mean-square deviation (RMSD) units in ChimeraX, use rmsLevel.

      CHIMERAXCopy

      volume #1.1.1.2 sdLevel 1.0 color blue
      

      

      • Here you can use color blue to assign the color.

      For an mFo-Fc difference map, you may want to set positive and negative levels:

      CHIMERAXCopy

      volume #1.1.1.4 sdLevel 3.0 color green sdLevel -3.0 color red
      

      [!TIP]

      If there's an axis indicator at the center in ChimeraX, you can turn it off with cofr show false.

   5. After a few simple adjustments to lighting and color, you'll have a beautiful figure.

      

Outro

There are many online tutorials on displaying and coloring cryo-EM density, but there seem to be fewer on crystal structures. I hope this helps.

Comments and discussion are welcome.