# MOLMOL Tutorial - Example 3

## Image

On this page, we will show how to create the following picture:

## Steps

`UserInterface 0 0 1 1 1 1`
(`Options->User Interface`)
Switch the Valuator Box and the Log Window off. We will not make use of these two here.

`ReadPdb 1pit.pdb`
(`File->Read Mol->PDB`)
Read the structures from the given file in PDB format.

The structures have to be superimposed for the next step. In our example they are already, otherwise we would do that here as explained in Example 1

`XMacStand sausage.mac`
(`File->Macro->Execute Standard`)
Use the standard macro for creating a sausage display. If you are interested in the detailed commands used to do all of the steps manually, have a look at this macro.

`DialSelect on`
(`Button:selection`)
Open the selection dialog.

`SelectMol 'name != "mean"'`
(`Dialog:Select`)
The macro created a mean structure. We can get rid of the original 20 structures now, so we select all but the mean structure...

`RemoveMol`
(`Edit->Structure->Remove Mol`)
... and remove them.

`DialStyle on`
(`Button:style`)
Open the style dialog.

`SelectBond ''`
(`Dialog:Select`)
`StyleBond invisible`
(`Dialog:Style`)
The bonds of the mean structure are still visible, select all bonds and make them invisible

`SelectAtom ''`
(`Dialog:Select`)
The standard orientation for BPTI is the one where the pricipal axes are aligned to the coordinate axes. So we select all atoms...

`Fit to_axes`
(`Edit->Fit`)
... and do the alignment.

We now have the basic sausage display. Now you will learn how to use "variable color", i. e. a separate color for each residue. We will use the secondary structure type for determining the color, it is also common to use physical properties like exchange rates.

`CalcSecondary`
(`Calc->Secondary`)
So we calculate the secondary structure first.

`PaintRibbon atom`
(`Prim->Ribbon->Paint`)
This causes the color of each sausage part to be taken from the atom that was used to define it. Because atoms also have a blue default color, there is no visible change yet.

`DialColor on`
(`Button:color`)
Open the color dialog.

`SelectAtom '@CA'`
(`Dialog:Selection`)
`ColorAtom 0.7 0.7 0.7`
(`Dialog:Color`)
The macro that we used took the CA atoms to define the sausage, so we have to set the color of the CA atoms. We first select all CA atoms and color them grey.

`SelectAtom '@CA & res.helix'`
(`Dialog:Selection`)
`ColorAtom 1 0 0`
(`Dialog:Color`)
Then we select all CA atoms within helices and color them red.

`SelectAtom '@CA & res.sheet'`
(`Dialog:Selection`)
`ColorAtom 0 1 1`
(`Dialog:Color`)
In the same way we color all CA atoms within a sheet cyan.

`BackColor 0 0 0`
(`Dialog:Color`)
Change the background color to black.

`PlotPar 21 29.7 18 0 500 0 1 1 0 3 1.0 75`
(`Options->Plot->Parameters`)
Adapt the plot paramters to our needs. Read the online manual page carefully, understanding these parameters is very important for using the program successfully!

`PlotTiff example3.tif`
(`File->Plot->TIFF`)
Create a TIFF plot. External tools were used for the conversion to GIF used for this page.

`WriteDump example3.mml`
(`File->Write Dump`)
Save the current state for later use.

`Quit no`
(`File->Quit`)
Quit the program. Because we already saved a dump file, there is no need for saving the program state again.

## Macro

The following is a summary of the executed commands, you can cut'n'paste it, edit it to your needs, and use it as macro:

    UserInterface 0 0 1 1 1 1
    ReadPdb 1pit.pdb
    XMacStand sausage.mac
    DialSelect on
    SelectMol 'name != "mean"'
    RemoveMol
    DialStyle on
    SelectBond ''
    StyleBond invisible
    SelectAtom ''
    Fit to_axes
    CalcSecondary
    PaintRibbon atom
    DialColor on
    SelectAtom '@CA'
    ColorAtom 0.7 0.7 0.7
    SelectAtom '@CA & res.helix'
    ColorAtom 1 0 0
    SelectAtom '@CA & res.sheet'
    ColorAtom 0 1 1
    BackColor 0 0 0
    PlotPar 21 29.7 18 0 500 0 1 1 0 3 1.0 75
    PlotTiff example3.tif
    WriteDump example3.mol
    Quit no

Last modified: Mon Jan 20 19:45:00 CST 2003