MOLMOL Tutorial - Example 1

Image

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

Steps

UserInterface
(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.

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

StyleBond invisible
(Dialog:Style)
When you want to show only part of the bonds, it's often most convenient to make everything invisible first and then "build up" the visible parts piece by piece. Everything is selected by default, so this will make all bonds invisible.

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

SelectBond 'bb'
(Dialog:Select)
Now we select all bonds in the backbone. bb is a shortcut for that, a so called "predefined property". Activate the HelpProp (Help->Prop) command for getting a list of all predefined properties. The definitons will also give you an impression of how the full MOLMOL expression syntax looks, in this tutorial we will mostly use shortcuts.

StyleBond line
(Dialog:Style)
Now we see only the backbone drawn with lines.

SelectAtom ':2-56 & bb'
(Dialog:Selection)
Fit to_first
(Edit->Fit)
The structures in the example file were already superimposed, but for demonstration purposes we do it again. We just use the backbone atoms of residues 2 to 56 for superposition, & is short for and.

You can now also try to rotate and zoom the structure. See HelpMouse (Help->Mouse) for a description on how to use the mouse.

DefPropRes 'inter' ':2,4,6,8,9,11,16,18,19,21-25,27,30,32-35,38,40,43,45,47,48,51,54' (Prop->Define->Res)
We will display the well-defined (interiour) sidechains different from the other ones. We could select them with the residue numbers each time, but we can also define our own shortcut (property) that we can use each time we want to select these.

SelectBond 'res.inter & heavysc'
(Dialog:Select)
We now select the bonds to heavy atoms in the well-defined sidechains using the inter property that we just defined (since we defined it for residues, we have to write res.inter if we want to use if for bonds) and the predefined property heavysc (for heavy sidechain).

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

StyleBond line
(Dialog:Style)
ColorBond 1 0 0
(Dialog:Color)
Draw the selected bonds as red lines. The commands take colors as RGB (Red-Green-Blue) values, the color dialog allows you to choose the most common colors by name.

SelectBond '! res.inter & heavysc'
(Dialog:Select)
Select the rest of the sidechains. ! is short for not.

StyleBond line
(Dialog:Style)
ColorBond 0 1 0
(Dialog:Color)
Draw the selected bonds as green lines.

SelectBond 'visible'
(Dialog:Select)
So far we just displayed bonds as lines, mainly because it makes the display much faster. We now select all visible bonds...

StyleBond neon
(Dialog:Style)
... and display them as neon (cylinder with round ends).

RadiusBond 0.15
(Button:bond rad)
Make the cylinders somewhat thinner.

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 example1.tif
(File->Plot->TIFF)
Create a TIFF plot. External tools were used for the conversion to GIF used for this page.

WriteDump example1.mol
(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
DialStyle on
StyleBond invisible
DialSelect on
SelectBond 'bb'
StyleBond line
SelectAtom ':2-56 & bb'
Fit to_first
DefPropRes 'inter' ':2,4,6,8,9,11,16,18,19,21-25,27,30,32-35,38,40,43,45,47,48,51,54'
SelectBond 'res.inter & heavysc'
DialColor on
StyleBond line
ColorBond 1 0 0
SelectBond '! res.inter & heavysc'
StyleBond line
ColorBond 0 1 0
SelectBond 'visible'
StyleBond neon
RadiusBond 0.15
PlotPar 21 29.7 18 0 500 0 1 1 0 3 1.0 75
PlotTiff example1.tif
WriteDump example1.mol
Quit no

Last modified: Jan 17, 1997