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Visualizing Molecular Structures with VMD

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Loading Structure Files and Interacting with Molecules

Overview

Teaching: 30 min
Exercises: 10 min
Questions

  • How to load PDB files into VMD?

  • How to view molecules interactively?

  • How to measure distances, angles and dihedrals?

Objectives

  • Learn how to load molecular structure files

  • Learn how to interact with molecules

  • Learn how get information about atoms and molecules

  • Learn how to measure distances, angles and dihedrals?

Starting VMD

Starting VMD on a cluster

Open a terminal: Applications –> System Tools –> Mate Terminal

module load StdEnv/2023 vmd
vmd

Starting VMD on Windows

Use the VMD desktop launcher.

Important: On Windows VMD starts in the installation directory. Users don’t have permission to write in this directory, so to begin using VMD change to your home directory. You can do it by typing cd in the VMD command window.

VMD user interface

Three windows will open:

Working with PDB files

As an example will be using X-ray crystallographic structure of human hemoglobin 1SI4.

Downloading files from Protein Data Bank

VMD can directly query PDB database. VMD-Main > Extensions > Data > PDB Database Query

Enter “1si4” and click Load into new molecule in VMD.

Hemoglobin rendered as sticks

Note: loading files from PDB is not possible from compute nodes on all clusters except Cedar because they are not connected to the Internet. Use the login nodes on these systems to download PDB files.

Opening a PDB file saved in your computer.

On a cluster you can download the example PDB file using the following command:

wget https://files.rcsb.org/download/1si4.pdb

If you are using VMD on your local computer you can navigate your browser to the URL above.

Once the file is downloaded, in the VMD Main window menu select File -> New Molecule. The Molecule File Browser window will open. Choose a molecule PDB file.

Understanding information about the loaded molecules

Load a second molecule (you can use the same pdb file), and make sure you have two molecules (ID 0 and 1) loaded.

VMD shows information about loaded molecules in its main window. This window displays:

There are four components to molecular status:

Fixing molecules

Customizing VMD sessions

A few settings often need to be changed from the defaults.

Interacting with molecules

Obtaining good views for molecules

Rotate, zoom in/out, translate, and set rotation center to get a desired view. Pressing any of these keys switches the mode of interaction. For example, when s key is pressed mouse cursor will change. In this mode click, hold and move on a trackpad/mouse will zoom in/out. If you zoomed too much and don’t see the molecule simply press the = key to reset view.

Action Hot keys
Rotate r
Zoom (Scale) s
Translate t
Reset View =
Set Center c

Working with Graphical Representations

Creating and modifying graphical representations

In the Graphical representations window you can create representations for selected atoms, choose drawing styles and coloring methods

Hemoglobin rendered as "New Cartoon"

Hemoglobin rendered as backbone with transparent surface

Selecting atoms

In order to make a figure that is clear and impactful, it is useful to display different components of a system using different representations. Selecting groups of atoms is the key to achieving this. Selecting atoms is easy, with lots of options.

What selections are available in the loaded molecule?

In the Graphical representations window go to Selections–>Keyword–>chain. VMD will display all chains in the selected molecule (A,B,C,D). Double click on the Value to select it. To select two or more chains you need to use a command.

Measuring distances, angles, and dihedrals

Use hot keys to measure distances, angles and torsions.

Action Hot keys
Print info about an atom 0
Label atom 1
Measure bond 2
Measure angle 3
Measure dihedral 4

How to delete or hide Labels?

Labels can quickly clutter display. How to delete or hide Labels when you don’t need them anymore?

Challenge

Reproduce the following figure. In this image we see chain A of the pdb entry 1SI4.

The figure shows:

  • protein (new cartoon)
  • residue HEM (orange licorice)
  • HEM atom FE (red CPK)
  • HEM ligand residue HIS (yellow licorice)
  • HEM ligand residue CYN (yellow VDW).

Hemoglobin protein with ligand Use the following selection keywords: chain, name, resname, same residue as within. You will also need to use logical operators and, not.

Solution

select chain A
chain A new cartoon, iceblue, aochalky

select HEM
chain A and resname HEM
licorice, colorid 3, aochalky

Select atom FE
chain A and name FE
VDW scale 0.4, colorid 1, aochalky

Select only FE ligands
not resname HEM and same residue as within 3 of name FE and chain A
licorice, colorid 4, aochalky

The previous command selected two FE ligands. How do we select only the small 2-atom FE ligand?
Pick any atom from this molecule. All information about the atom will be printed in the VMD terminal window.

select CYN
chain A and resname CYN
surf, colorid 4, aochalky

  • save your work: File->Save visualization state.

Changing default colors

There are 1041 colors available in VMD, with color ids ranging from 0 to 1040. The first 33 are named colors. The remaining group of 1008 are colors used in color maps. There are no names for the specific colors in this group.

Each of the first 33 colors can be modified: Graphics–>Colors–>Color Definitions

Saving your work

A VMD state file is a TCL script that contains all commands used in creating a visualization. You add new commands to a visualization script as you work on it, so it becomes longer and longer. When VMD scripts are executed, they go through all your steps. It is common for intermediary steps to be just trial commands that are not needed to recreate the final version. For example, you created and then deleted some representations, changed colors several times.

In the future, you might want to reuse the visualization scene as a template for visualizing similar molecules. It is a good idea to inspect the visualization state file and keep only the commands necessary to recreate the final scene. In this way, it will remain clear and readable.

Customizing VMD sessions

At startup VMD load a set of default options. You may find that they are not optimal for your work, and you need to change them every time you start a new visualization. Once you have changed settings to your liking you can make them permanent.

Saving current settings

Using the following steps, you can save current settings: Extensions->VMD Preferences -> Write setting to VMDRC

Managing VMDRC files

VMD preferences are saved in ~/.vmdrc file. VMD creates a very long file containing hundreds of all available settings, even the ones that are using global default values. You may find useful to create a short version of .vmdrc containing only settings that you want to change. A .vmdrc file is just a text file and it can easily be edited manually with any text editor.

Let’s open it. Settings are organized in sections. You don’t want to change default colors, materials or menus. So you can safely delete these sections and leave only display parameters and molecular representations.

As an example, a .vmdrc file might look like this:

      # VMD settings: file ~/.vmdrc

      # Turning-on of menus
      menu main on

      # Change display defaults
      display reposition 100 600
      display resize 672 682
      display projection Orthographic
      display depthcue off
      display rendermode GLSL
      display ambientocclusion on
      axes location Off
      color Display Background white

      # Default material
      mol default material Diffuse

      # Configure keyboard shortcuts
      user add key o {display projection orthographic} 
      user add key p {display projection perspective}

Key Points

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