Protein Evolution
Friday 30th January 2009
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
- it is possible to set up your computer so that simply clicking on
the icon representing the structure file (typically with the ending
.pdb or pse), the file will open in PyMOL
- it may also be possible to just drag-and-drop the structure file
onto the PyMOL main-window
- something that should be standard and work on all operating
systems is to go via the File->Open on the Menu-Bar. Additionally,
this method can be used to add additional structures from other files
to the same viewing space
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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