DINO: Visualizing Structural Biology
Table of Contents
User Manual

1 Quickstart

This chapter will quickly go through a typical DINO script, introducing concepts and leaving details to the following sections of the manual. The files used here are the sea-hare myoglobin structure 1MBA (Bolognesi et. al., 1990) and the corresponding MSMS surface files (to be found on the DINO homepage).


Start up DINO in the directory with the files and enter the following commands at the prompt dino>

load myo.pdb

The structure in the file myo.pdb is loaded from disk. This creates a dataset called myo which is used in subsequent commands to adress the structure.

Nothing is visible on the screen yet. We first need to create an object which will be displayed in the main graphics window. To do this, the dataset command new is used. We will name the object all because we do not apply a selection, hence the object contains all atoms of the structure:

.myo new -name all

There is still nothing visible: we need to center the object on the screen. This is accomplished with the scene command center , using a recursive subprompt. Right now, it is important to realize that [.myo] returns the geometric center of the structure:

scene center [.myo]

The front and back clipping planes are adjusted:

scene autoslab 

The protein should now be visible and react to input from the mouse; hold the left mouse button down in graphics window and move the mouse or try the dials (if present).

Let us create a specific object, e.g. just the heme group. This time new is called with a selection:

.myo new -name hem -sel rname=HEM

The graphical appearance is modified with the object command render :

.myo.hem render custom,sr=0.35,bw=0.15

We can center on the object or on a specific atom, in this case the heme iron

scene center [.myo.hem]      // center on object
scene center [.myo:148.FE] // center on atom

Try these different render modes and parameters

.myo.hem render cpk
.myo.hem render detail=2
.myo.hem render detail=6 
.myo.hem render simple

Since we have the heme as an individual object, we can modify our original object all to not have the heme anymore by using the object command renew combined with a selection:

.myo.all renew -sel not rname=HEM

To change colors of individual atoms, the object command set with a selection is used, e.g. to color all carbons in green:

.myo.all set color=green -sel aname=C*

We will look at more syntax. First we turn off the display of the protein object

.myo.all hide

Now we will generate a sphere of residues surrounding the heme. We create a new object and use the within operator <> together with an object as selection criteria. Additionally - since we already have the heme as an object - we exclude the heme from the selection

.myo new -name sphere -sel 10<>.myo.hem and not rname=HEM

The selection mechanisms has picked out some individual atoms which are not connected to anything and are displayed as crosses. To tell DINO that we want to select residues, change the selection mode of the dataset to residue (default is atom ), and simply renew the object, it will remember its selection syntax:

.myo set smode=residue
.myo.sphere renew

Let us turn to the other object type for structure datasets: the trace. We will first hide the sphere object

.myo.sphere hide

A trace object is created and colored in purple:

.myo new -name ca -type trace
.myo.ca set color=purple

trace objects can also be rendered in different ways, e.g. as interpolated tubes:

.myo.ca render tube,bw=0.3 
scene center [.myo.ca]

try also following render modes and parameters

.myo.ca render sline
.myo.ca render tube,bw=1.0
.myo.ca render simple

This concludes the structure dataset part, we will go on to the surface:

.*.* hide  // hide everything

A surface generated with MSMS is loaded and named surf . Then a surface object is created, centered on the screen and the clipping planes are adjusted

load myo -type msms -name surf 
.surf new -name all 
scene center [.surf.all] 
scene autoslab

To do more with the surface, we can attach it to a structure dataset:

.surf attach .myo

Now each surface vertex (point) carries information about the atom closest to it, so we can use atom-selection statements for the surface object

.surf.all set color=blue -sel rname=LYS,ARG 
.surf.all set color=red -sel rname=ASP,GLU

A second surface was calculated, without the heme group present in the structure. This surface is loaded, a new object is generated and centered on the screen:

.*.* hide
load myo_apo -type msms -name surfa 
.surfa new -name all 
scene center [.surfa.all]

Since the surface was calculated without the heme, we will turn the heme object back on and try to find it in the structure by rotating the surface around.

.myo.hem show 
.myo.hem render custom,sr=0.3,bw=0.3,detail=3

To take a closer look on the surface that surrounds the heme, we will create a new object: the part of the surface that lies within 10 of any atom of the heme

.surfa.all hide 
.surfa new -name hem -sel 10<>.myo.hem

We can now turn on the sphere object and render the surface transparent for a nice view:

.myo.sphere show 
.surfa.hem render t=0.5

The new surface can also be attached to the structure

.*.* hide 
.surfa.all show 
.surfa attach .myo

To see what has happened during the attachment, we will color the complete surface in yellow that is part of the protein:

.surfa.all set color=yellow -sel $protein

In the groove of the heme the surface is partially white. The reason for this is that the heme was included in the attachment. To avoid this the structure dataset is restricted, and then the attachment is performed, ignoring all restricted atoms. The surface is un-attached first.

.myo restrict not rname=HEM
.surfa attach none
.surfa attach .myo
.myo restrict

Same command as above, but now the complete surface should be yellow

.surfa.all set color=yellow -sel $protein


This concludes the quickstart. Please visit the DINO homepage for more tutorials.