Week 7 - Swiss-Pdb Viewer (SPDBV)¶

Swiss-Pdb Viewer (SPDBV)

Download:

https://spdbv.unil.ch/disclaim.html

Rotating and magnifying a protein¶

Example 1: View PDB ID `3PDT` in SPDBV¶

Download the PDB file for 3PDT.
Open Swiss-Pdb Viewer.
File → Open PDB file → 3PDT

Alternative:

File → Import
Type 3PDT into the Name box.
From Grab from Server menu, click PDB file (not Grab from disk).

Import file

Notes:

SPDBV opens molecules in sticks style by default.
To rotate the protein: left click and drag.
Three icons under the menu bar are useful for switching between positioning, magnification, and rotation modes.

Swiss-Pdb Viewer controls

Position | Magnification | Rotation

You can switch between these modes either by clicking the icons or pressing Tab.
Rotation mode is the default.
Magnification:
Click the magnification icon, then left click and drag to zoom.
Drag forward to zoom out; drag backward to zoom in.
Repositioning:
In rotation and magnification modes: right click + drag.
In position mode: left click + drag.

Selecting¶

Example 2¶

Selecting residues¶

Select → Group Kind → Ser (S)
Color → Selection
Select → Group Property → Acidic
Color → Selection
Color → Secondary Structure → Helices
Color → Selection

Selection helpers:

Invert selection:
Select → Inverse selection, or
Alt+1
Select all:
Select → All, or
Ctrl+A
Select none:
Select → None, or
Alt+0
Select solvent accessible residues:
Select → Accessible Residues
Return to original colors:
Select none → Color → CPK

Picking residues from the 3D view:

Select → Pick on Screen → click residues
Select 3 residues on screen, then Color → Selection
Go back to CPK colors

Selecting ligand¶

Select → Group Kind → HETATM
Color → Selection

To select residues around ligands:

Select → Neighbor of selected residues
Check Add to Selection groups
Distance: 5.000 Å

Display radius

Color → Selection

SPDBV also allows selection of:

residues making clashes
side chains lacking proper hydrogen bonds
chain breaks

(these are available under the Select menu)

Selecting sequences¶

Alignment window:

Wind → Alignment
The Alignment window shows the full protein sequence.
Select sequences by left click + drag.
To select sequences from different parts:
Ctrl + left click + drag

Control panel:

Wind → Control Panel
Displays the amino acid sequence vertically.
Left click an amino acid to select it (its color turns red from black).
Select a range by left click + drag.
To select separate sequences:
Ctrl + left click + drag

Finding sequence¶

Edit → Find Sequence, or Ctrl+F
Find the sequence IALS.

Coloring¶

To color selected residues from Control Panel:

Click the square on the right side of the amino acid name.
Choose a color in the pop-up window.

Residue color

Other coloring tools:

Color → Type
Colors consecutive residues with different colors.

B-factor coloring:

SPDBV has a coloring tool that colors residues according to B-factor. B-factor is defined by Yuan Z. (2005) et al. as:

“The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics”.

B-factor coloring provides information about movable parts of the protein.

Color scale: blue → green
Green residues are more movable than blue parts.

Negative residues:

Color → Custom Scale → Negative
Colors negative residues red.

To identify which amino acid the red parts correspond to:

Click the "Leu 41 ?" icon on the toolbar.

Toolbar residue/atom info

In this mode you can see the residue and atom name when you move the cursor over the molecule.

Click a residue to label it.

Secondary structure coloring:

Color → Secondary Structure
Helix: red
β-sheet: yellow
Turns: gray

Solvent accessibility coloring:

More accessible parts: red
Less accessible parts: blue
Intermediate parts: blue → red gradient

Energy-based coloring:

Color → Threading Energy
Dark blue: low energy (residue is happy with its environment)
Red: high energy (residue is less happy)
Color → Force Field Energy
Computed with a partial implementation of the GROMOS force field.
Blue: low energy
Red: high energy
Colors are scaled automatically from lowest to highest (blue-green / green-red).
Useful during refinement to identify distorted parts of the protein.

Build¶

Break Backbone¶

Breaks the peptide bond between C and N.
Build → Break Backbone → pick a backbone N or C by clicking it.

Ligate Backbone¶

Creates a peptide bond between C and N.
Build → Ligate Backbone → pick the bond you have just broken to ligate it back.

Add residue¶

Add an amino acid residue to an alpha carbon.
Build → Add residue → click an alpha carbon.
Choose an amino acid from the list (e.g., His).

SPDBV shows possible interactions of the added residue as dashed lines.

Add Hydrogens¶

Build → Add Hydrogens
Displays hydrogen atoms in light blue.

Remove Selected Residues¶

Select → Pick on Screen
Pick two residues.
Build → Remove Selected Residues

Tools¶

H-bonds¶

Tools → Compute H-Bonds
Displays hydrogen bonds as green dashed lines.

Molecular Surface¶

Tools → Compute Molecular Surface

To remove the surface:

File → Discard → Surface

Electrostatic Potential¶

Tools → Compute Electrostatic Potential
Computes and displays electrostatic potential surface around the molecule.

Threading Energy¶

Threading energy is a criterion of reasonableness that reflects whether the environment of each residue in the model matches what is found for the same residue type in a representative set of protein folds.

For a given residue, a small value of threading energy implies a reasonable environment.

Examples of residues that may have high threading energies:

A hydrophobic residue on the surface of a model
An ionic residue buried without compensating charge in a hydrophobic core

SPDBV calculates threading energy and gives the results as a curve in the alignment window.

Tools → Compute Energy (Threading)
Open alignment window: Wind → Alignment
Click on the arrow head near the question mark on the alignment window.

Alignment curve (small)

You will see a curve for threading energies calculated for the amino acid sequence.

Alignment curve (large)

Force Field Energy¶

Computed with a partial implementation of the GROMOS96 force field.
You can choose which interactions to compute (bond, angles, improper, electrostatic, etc.).

Steps:

Tools → Compute Energy (Force Field)

Like threading energy, force field energy can be visualized as a curve in the alignment window. A report for energy calculation of each amino acid is shown in a separate window.

Distance measurement¶

Distance measurement

Measures distance between two atoms.
Click the icon, then click atom 1 and atom 2.

Angle measurement¶

Angle measurement

Measures the angle between three atoms.
Click the icon, then click three atoms.

Omega / Phi / Psi and torsion angle measurement¶

Omega / Phi / Psi

Measures omega, phi, and psi angles around the selected atom.
Click the icon, then pick one atom.
The angles will be displayed below the toolbar.

Torsion measurement

Press Ctrl + left click on the icon to measure the torsion angle of 4 atoms.
The torsion angle will be displayed below the toolbar.

Labeling¶

Labeling tool

Labels atoms with the amino acid they belong to and the atom name.
Click the icon, then pick one atom.

Pick atom

Neighbor of selected residues¶

Neighbor tool

Displays residues around the selected residue.
Click the icon, pick a residue.
Specify the distance in the pop-up.
Press Enter.

Centering¶

Centering

Centers the selected atom and repositions the other atoms accordingly.

Fitting a molecule onto another¶

Fitting

Fits a selected molecule to another.
Requires two molecules and three reference atoms from both structures.

Example 2: Fit F2P and HX5¶

Fit:

1,6-di-o-phosphono-D-allitol (F2P)
D-xylitol-5-phosphate (HX5)