Tutorials
Quickstart
Downlad this script with all is input files: myo.tar.gz
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
load myo.pdbNothing 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 allThere 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 (see shell command below). 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 (see scene commands below)
scene autoslab scene set fogd=0.5The protein should now be visible and react to input from the mouse (e.g. hold left mouse button down in graphics window and move mouse) or 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=HEMThe graphical appearance is modified with the object command render
.myo.hem render custom,sr=0.35,bw=0.15We can center on the object or on a specific atom, in this case the heme iron
scene center [.myo.hem] scene center [.myo:148.FE]Try these different render modes and parameters
.myo.hem render cpk .myo.hem render detail=2 .myo.hem render detail=6 .myo.hem render simpleSince 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 and a selection
.myo.all renew -sel not rname=HEMTo change colors of individual atoms, the 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 hideNow 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=HEMThe 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)
.myo set smode=residueOne more trick. Instead of excluding the heme for each selection, we can restrict it from the dataset so it will not be taken into consideration for all of the following commands
.myo restrict not rname=HEMNow we renew the sphere object. Note that the object remembers the selection specified with the new command above, so we can omit it here.
.myo.sphere renewRestrictions can be turned of again by calling restrict alone:
.myo restrictLet us turn to the other object type for structure datasets: the trace. We will first hide the sphere object
.myo.sphere hideA trace object is created (use echo $protein to look at this predefined variable) and colored in purple
.myo new -name ca -type trace -selection $protein .myo.ca set color=purpletraces object 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 simpleThis concludes the structure dataset part, we will go on to the surface
.*.* hideA 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 autoslabTo do more with the surface, we can attach it to a structure dataset:
.surf attach .myoNow 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,GLUA second surface was calculated, without the heme group present in the structure.
.*.* hideThis surface is loaded, a new object is generated and centered on the screen
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=3To 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.hemWe can now turn on the sphere object and render the surface transparent for a nice view
.myo.sphere show .surfa.hem render t=0.5The new surface can also be attached to the structure
.*.* hide .surfa.all show .surfa attach .myoTo 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 $proteinIn 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 (as above), and then the attachment is performed: The attachment ignores all restricted atoms. Just to be sure, the surface is un-attached first.
.myo restrict not rname=HEM .surfa attach none .surfa attach .myo .myo restrictSame command as above, but now the complete surface should be yellow
.surfa.all set color=yellow -sel $protein
Download this tutorial: myo.tar.gz