# MOLMOL Tutorial - Example 2

## 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.

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

`SelectMol 'num > 1'`
(`Dialog:Select`)
We only want to make a schematic drawing of the first of the 20 structures, so we select all but the first...

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

`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.

`XMacStand ribbon.mac`
(`File->Macro->Execute Standard`)
Use the standard macro for creating a ribbon display. If you are interested in the detailed commands used to do all of the steps manually, have a look at this macro. We could have used `Button:ribbon` instead, but this would have done an automatic determination of the secondary structure first, while we preferred to use the definitions from the PDB file in this case.

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

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

`SelectPrim 'num = 10'`
(`Mouse`)
The second helix seems to be defined too long. So we select it by clicking on it with the mouse...

`LengthPrim 46 55`
(`Prim->Length`)
... and make it half a residue shorter at each end.

You could now use commands like `SplitRibbon`, `StyleRibbon`, `SizeRibbon` and `ColorPrim` to modify the display, but for the moment we are happy with the default.

`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 example2.tif`
(`File->Plot->TIFF`)
Create a TIFF plot. External tools were used for the conversion to GIF used for this page.

`WriteDump example2.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
    DialSelect on
    SelectMol 'num > 1'
    RemoveMol
    SelectAtom ''
    Fit to_axes
    XMacStand ribbon.mac
    DialColor on
    BackColor 0 0 0
    SelectPrim 'num = 10'
    LengthPrim 46 55
    PlotPar 21 29.7 18 0 500 0 1 1 0 3 1.0 75
    PlotTiff example2.tif
    WriteDump example2.mol
    Quit no

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