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

Reto Koradi, kor@mol.biol.ethz.ch