Graphical representation

using commands

example for a standard CPK representation

mol selection {all}

mol representation CPK 1.100000 0.300000 20.000000 16.000000

mol color Name

mol addrep top

what this does

select everything

CPK is VDW and bonds

sphere_scale=1.1 bond_radius=0.3 sphere_res=20 bond_resolution=16

select how colour is choosen

now apply the changes

other representations include

mol representation CPK 1.15 0.3 30.0 16.0

sphere scale, sphere resolution, bond radius, bond resolution

mol representation VDW 0.30 30.0

sphere scale, sphere resolution

mol representation DynamicBonds 1.200000 0.200000 12.000000

distance cut-off, bond radius, bond resolution

mol representation HBonds 3.0 30.0 3.0

more complex selections
for example atoms within 2.89 of central Cl that are H atoms ie (Cl-H rdf)

mol selection (within 2.89 of element Cl) and name "H"

mol color ColorID 2

mol addrep top

using the gui

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when overlaying structures.

Structure model

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

Settings for Licorice representation in VMD
Before	After
VMD default settings	Our default settings

Please note there are many other model representations you can use.

Model colour

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.