Limit selection to one monomer: not (protein or nucleic or resname HOH).Selecting hetero atoms: not (protein or nucleic or resname HOH).Selecting an atom: index (starts from 0), serial (starts from 1).Selecting a residue: residue (starts from 0), resid (read from a file).Most often used selection keywords are noh, backbone, protein, nucleic, resname, resid, index.Selecting atoms is easy, with lots of options. Selecting groups of atoms is the key to achieving this. In order to make a figure that is clear and impactful, it is useful to display different components of a system using different representations. Most useful draw styles: NewCartoon, QuickSurf, Surf, Licorice, VDW, HBonds.Double click to turn representations on/off without deleting them.Make the surface transparent by changing material to GlassBubble.Create a new representation and change its drawing method to QuickSurf.Try another drawing method: Drawing method –> Tube.Try to get a better illumination by moving lights: Mouse-> Move Light.Navigate to Graphics –> Representations.In the Graphical representations window you can create representations for selected atoms, choose drawing styles and coloring methods Working with Graphical Representations Creating and modifying graphical representations

If you zoomed too much and don’t see the molecule simply press the = key to reset view. In this mode click, hold and move on a trackpad/mouse will zoom in/out. For example, when s key is pressed mouse cursor will change. Pressing any of these keys switches the mode of interaction. Rotate, zoom in/out, translate, and set rotation center to get a desired view. Interacting with molecules Obtaining good views for molecules These ray-tracing options enable photorealistic rendering. Display ambientocclusion on and Mol default material Diffuse.Most of the time, it is not desirable and there are better alternatives. This is achieved by blending distant objects into the background color.

The use of depth cues can enhance perception of depth and distance. In most cases you don’t want axes to appear in figures prepared for publication. Due to this, it is difficult to determine the relative size and dimensions of distant objects in perspective mode. The angle of view, distance, and focal length of a camera lens make lines of identical length appear different in perspective mode. The orthographic projection allows us to get a better sense of the distance between objects and their relative sizes. It will improve if more CPUs are available, but the best of course is to use a GPU. Performance is better now but still slow. Try rotating molecule and observe rendering speed. Load 6n4o.pdb file, and create a NewCartoon representation.This mode renders faster and produces better images than “Normal” mode.

The GLSL mode turns on OpenGL extensions implementing programmable shading and transparency for higher quality molecular graphics.

Try using mouse to rotate/translate molecules.Ī few settings often need to be changed from the defaults.

Several commands such as Animate operate on all active molecules. Some commands such as centering are applied only to the top molecule. Top indicates the default molecule used in the mol text command. There are four components to molecular status: VMD shows information about loaded molecules in its main window. Load a second molecule (you can use the same pdb file), and make sure you have two molecules (ID 0 and 1) loaded. Understanding information about the loaded molecules The Molecule File Browser window will open. Once the file is downloaded, in the VMD Main window menu select File -> New Molecule. If you are using VMD on your local computer you can navigate your browser to the URL above. On a cluster you can download the example PDB file using the following command: Opening a PDB file saved in your computer. Use the login nodes on these systems to download PDB files. Note: loading files from PDB is not possible from compute nodes on all clusters except Cedar because they are not connected to the Internet.

Downloading files from Protein Data BankĮnter “1si4” and click Load into new molecule in VMD.

VMD command window, show info and run text commandsĪs an example will be using X-ray crystallographic structure of human hemoglobin 1SI4.

VMD Main, work with molecules and trajectories, start interfaces and extensions.

VMD OpenGL Display, display and interact with molecules.

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

Saving vmd files