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