Bodil Tutorial

This tutorial is composed of three parts, in which the user will go through the very basics of Bodil. First, four protein crystal structures are searched from the Protein Data Bank and then one of these structures is viewed in Bodil. Second, structures are superimposed and a structure-based sequence alignment is visualized. Finally, a multiple sequence alignment is done with program MALIGN. Based on this alignment, a homology model is made using the program HOMODGE, which is implemented in Bodil.

Some instructions for the tutorials:
[MENU] stands for a menu option in a window that is indicated in context.
[DIALOG] means that a dialog box opens and the user should select from this box.
LMB = left mouse button
MMB = middle mouse button
RMB = right mouse button
The default mouse button in this tutorial is LMB. Therefore, if no other mouse button is indicated, the user should use the LMB. The tutorials are recommended to be compleated in the correct order, from 1 to 3.

NOTE: All the files that will be needed during the Bodil Tutorial are provided with the tutorial package.Therefore, it is not obligatory to fetch the files from the www, however, instructions on how to perform the database searches will also be provided.



Tutorial 1

Searching structures from Protein Data Bank

In the world wide web, go to page http://www.rcsb.org/pdb/. This is the main page for Protein Data Bank. Enter keyword integrin into the search box and start the search. On the result page, search the structure with PDB code 1AOX. To see the details of this structure, click { EXPLORE }. To download the structure file, click the link Download/Display File . In the Download the Structure File section, select PDB Format: no compression. Save the file in text format and with name 1AOX.pdb. Finally, search for the integrin structures with PDB codes: 1CQP, 1JLM and 1PT6, and save these structures the same way as before.

Visualizing a structure in Bodil

The Bodil Main Window is the main interface for the program. All the other modules can be started from this window. Open the Graphics (3Dview) window from [MENU] View - 3Dview. Open also the Structure Editor window from [MENU] View - StructureEditor.


Tutorial 2

In this tutorial you will learn how to superimpose structures and how to visualize sturcture-based sequence alignments.


Tutorial 3

In the third tutorial you will learn how to make a multiple sequence alignment with MALIGN. In addition, you will make a homology model with HOMODGE.


Improve the quality of graphics in Bodil

The configuration editor plugin allows user to view and edit configuration settings that currently exists in Bodil memory. The plugin can be activated from Bodil Main Window [MENU] Preferences - Options. This opens a Config management window, where the configuration settings can be edited. Click with any mouse button the line that you want to edit and an "Edit selection" DIALOG opens. In DIALOG type the desired modification and click OK. The modification will take place in windows that are opened after the modification. With the "Reload" button the settings from configuration files will be reread.




References:


Updated: 16th April, 2004 Susanna Repo