MOLMOL Tutorial - Example 4

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 plot of the surface 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 pdb_charge.mac
(File->Macro->Execute Standard)
For calculating the electrostatic potential, it is very important to have the proper charge for all residues. Since the charges are normally not given in a PDB file, we call this macro that does the typically necessary changes, like GLU to GLU-. You should manually check whether all charges are correct before calculating the potential. In this case we notice that we are missing the charges at the termini, because the sequence in the file just starts with an ARG and ends with an ALA.

SelectRes ':1'
(Dialog:Select)
So we select the first residue...

ChangeRes atoms 'NARG'
(Edit->Structure->Change Res)
And convert it to NARG, the form of ARG with an N-terminal group, maintaining the old coordinates.

CalcAtom 'HN*'
(Calc->Atom)
It is not really needed for this example, but for demonstration purpose we calculate the coordinates of the HN2 and HN3 that are missing because these atoms did not exist in the ARG residue that we originally read from the file.

SelectRes ':58'
(Dialog:Select)
The same way we select the last residue...

ChangeRes atoms 'CALA'
(Edit->Structure->Change Res)
... convert it to CALA, the form of ALA with a C-terminal group...

CalcAtom 'O*'
(Calc->Atom)
... and calculate the coordinates of OA and OB. These we actually need, because they hold charges.

SelectAtom 'heavy'
(Dialog:Select)
We only use the heavy atoms for calculating potential and surface. If protons are also used, they "dampen" the charges visible at the surface, which leads to less clear pictures.

CalcPot (vdw) (simplecharge) 2 80 1.4 2 2 10 zero 'bpti.pot'
(Calc->Potential)
Now we can calculate the electrostatic potential, storing the result in the file bpti.pot. Check the help page for details about the arguments. We accept the defaults, except for the charge, where we choose the simple model without partial charges, only charges located on one or two atoms of each charged residue. Note that the current drawing precision (see DrawPrec) determines the grid width for the calculation, we keep the default of 3 that leads to a grid spacing of 1 Angstrom.

AddSurface (vdw) contact 1.4 shaded safe
(Prim->Surface->Add)
Calculate the contact surface.

ReadPot bpti.pot
(File->Read Potential)
Read the previously calculated potential. The values are now mapped onto the surface, so this step has to be executed after calculating the surface.

PaintSurface pot 1.4 '-0.3 1 0 0 0.0 1 1 1 0.3 0 0 1'
(Prim->Surface->Add)
Define how the surface is colored. We choose calculating the color from the previously read potential. The second argument is not used in this case, the third argument gives the mapping from potential to color, see the help page for details.

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 example4.tif
(File->Plot->TIFF)
Create a TIFF plot. External tools were used for the conversion to GIF used for this page.

WriteDump example4.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
DialSelect on
SelectMol 'num > 1'
RemoveMol
SelectAtom ''
Fit to_axes
XMacStand pdb_charge.mac
SelectRes ':1'
ChangeRes atoms 'NARG'
CalcAtom 'HN*'
SelectRes ':58'
ChangeRes atoms 'CALA'
CalcAtom 'O*'
SelectAtom 'heavy'
CalcPot vdw simplecharge 2 80 1.4 2 2 10 zero 'bpti.pot'
AddSurface vdw contact 1.4 shaded
ReadPot bpti.pot
PaintSurface pot 1.4 '-0.3 1 0 0 0.0 1 1 1 0.3 0 0 1'
PlotPar 21 29.7 18 0 500 0 1 1 0 3 1.0 75
PlotTiff example4.tif
WriteDump example4.mol
Quit no

Last modified: April 22, 1997