Protein Evolution

Friday 30th January 2009

Molecular Biotechnology Center [MBC], Torino, Italy

ELLS LearningLAB: Molecular evolution: modern evidence for Darwin's theory  

Aidan Budd and Francesca Diella

Getting PyMOL

Recently-released version of PyMOL must be bought from DeLano Scientific Limited.

However, the no-longer-supported release 0.99 is free for all to download and use for Windows, Macintosch, and Linux.

Further Information and Tutorials on PyMOL

There are several sources of information on PyMOL on the internet

Using PyMOL

Note that the instructions and screen-shots shown below are for the Macintosh version 0.99 of PyMOL - they will be similar, with hopefully only slight differences, on the Windows and Linux versions of the software.

To obtain the full functionality of this software, you will need a three-button mouse (e.g. for Macintosh you could be using a "Mighty Mouse").

Loading a Structure into PyMOL

There are several ways to load a structure file into PyMOL

Viewing the Protein Sequence

Once you have loaded a structure file into PyMOL you may want to also see the sequence of any peptides (and information about the names of residues from other non-peptide molecules macromolecules) of the chains included in the structure file.

To do this, you need to switch on the "Sequence On" option, accessed via the "Display" Menu-Bar menu

This will then display the sequence of the chains as shown below - with the sequence residues coloured the same as the corresponding regions of the structure

Selecting a Sequence Region

To select (and thus highlight/change colour/change representation of) amino acid residues in the sequence, simply select the residues you want to highlight using the left mouse button - or to select several at the same time, just drag along the sequence while holding the left mouse button.

The selected sequence residues will be highlighted in the sequence - at the same time, the regions of the structure corresponding to these residues will also be highlighted by adding purple dots to the selected atoms

Changing the Colour of a Selection

To change the colour of the selection, click with the left mouse button over the "C" box associated with the selection

Then choose the colour you want for the selection - below we choose magenta as the new colour

The selected amino-acid residues, both on the sequence viewer, and on the structure, have changed colour to magenta

Aligning Structures/Selections

To align to structures/regions of structures with each other, left click with the mouse over the "A" ("Action") button for the object or selection you want to align

Here you choose the "Align" action, then usually "to selection" (although try "to molecule" if this option doesn't work), and then select the name of the selection you want to align to

This will carry out a (rather simple and not very accurate) alignment of the structure of the two selections - as seen below

Saving a PyMOL Screenshot/Image

Sometimes you will want to save the image you have obtained in the PyMOL view screen as a separate image file. To do this, use the menu-bar's File->Save Image option

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