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Use ChimeraX to plot the crystal structure of small molecule density

#ChimeraX#X-Ray#Tutorial#Scientific illustration8
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This document provides a guide for using ChimeraX to visualize electron density maps alongside crystal structure data, specifically using the example of PDB file 7VH8. ### Key Steps: 1. **Installation**: Install the Clipper tool in ChimeraX either through the graphical interface or by using the command `toolshed install clipper`. 2. **Loading Files**: Open the PDB file and drag the corresponding MTZ file into ChimeraX, selecting the appropriate PDB. 3. **Density Visualization**: - Change the background color to white with `set bgcolor white`. - Select the small molecule using `sel #1.2:4WI`. - Display density around the selected molecule with the command `clipper isolate sel surroundDistance 0 contextDistance 5 maskRadius 2.5 hideSurrounds true focus true`. ### Parameters Explained: - **surroundDistance**: Distance to include additional atoms for map coverage. - **contextDistance**: Distance for showing additional context atoms. - **maskRadius**: Radius for the map mask. - **hideSurrounds**: Hides atoms outside the surroundDistance. - **focus**: Resets the view to center on the coverage area. ### Contour Levels: - Differences in contour level representation between Coot and ChimeraX are noted, with options to set levels in standard deviation or root-mean-square deviation units. ### Final Adjustments: - After adjusting lighting and colors, a visually appealing image can be created. The document concludes by encouraging discussion and sharing resources for visualizing cryo-EM densities and crystal structures.

Intro#

You need:

  1. ChimeraX installed
  2. Crystal structure coordinate PDB file
  3. Corresponding electron density mtz file for the PDB file

This article takes 7VH8 as an example, referring to this article to obtain the PDB and MTZ files.

TL;DR#

  1. Open ChimeraX and install Clipper, there are two installation methods:

    1. In the graphical interface, find the installation in Tools -> More Tools....
    2. Execute the command toolshed install clipper to install.

  2. After opening the PDB file, drag the mtz file in, a pop-up will appear, select the corresponding PDB.
    Select the corresponding PDB file
    It should look like this after opening:
    Import PDB and MTZ files

  3. Display density:

    1. First, change the background color to white:

      set bgcolor white

    2. Then select the small molecule:

      sel #1.2:4WI

    3. Display only the density near the small molecule:

      clipper isolate sel surroundDistance 0 contextDistance 5 maskRadius 2.5 hideSurrounds true focus true
      ParameterDescription
      selRefers to the currently selected atoms (i.e., small molecule)
      surroundDistanceSpecifies the distance to extend the selection, default is 0 Å. This parameter determines which additional atoms are included to calculate the map coverage area beyond the selected atoms.
      contextDistanceThis parameter sets the distance of the additional context area displayed, default is 5 Å. These atoms will be displayed but will not be covered by the map.
      maskRadiusSpecifies the radius of the map mask, default is 3 Å. This determines how far the map extends around the selected area.
      hideSurroundsIf true, atoms outside the surroundDistance range will be hidden (cartoon display is unaffected)
      focusIf true, the view will reset and center on the coverage area

      Display density near the small molecule

    4. Adjust the Contour Level and assign colors:

      It is important to note that there are differences in the Contour Level used by Coot and ChimeraX:

      SoftwareContour Level
      CootBy default, uses standard deviation (sigma) units to represent contour levels (though displayed as rmsd in the software).
      When setting the Contour Level to 1.0 in Coot, it actually represents the area where the density value is greater than or equal to the average density plus 1.0 standard deviation.
      ChimeraXTypically represents contour levels in absolute electron density values (electron/ų).
      When running the command volume #1 level 1.0, it indicates the area where the density value is equal to or greater than 1.0 electron/ų.

      Therefore:

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

      • If you want to represent the contour level in ChimeraX in root-mean-square deviation units, you can use rmsLevel.

      volume #1.1.1.2 sdLevel 1.0 color blue

      Contour Level

      • Here you can use color blue to assign color.

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

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

      [!TIP]

      If there is an indicator of the tri-axis center in ChimeraX, you can turn it off with cofr show false.

    5. After making simple adjustments to lighting and color, a beautiful image is completed.
      Final image

Outro#

There are many tutorials online teaching how to display and color cryo-EM density, while there seem to be fewer for crystal structures. I hope this helps you.

Feel free to leave comments for discussion.

This article is synchronized and updated by Mix Space to xLog. The original link is https://xxu.do/posts/x-ray/Using-ChimeraX-to-plot-crystal-structure-small-molecule-density

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