Use of molecular visualisation in the teaching practice
Moleküler Görüntüleme Çalıştayı

Workshop (Course)
Dokuz Eylül University, 2-3-4 April, 2012

Dates: Monday 2nd April, Tuesday 3rd April, Wednesday 4th April

Location: DEU School of Medicine Computer Laboratory

Duration: 15 hours (+ 2 hours evaluation)

Hoşgeldiniz!

Your guide in this course:

Prof. Angel Herráez
Dep. Biochemistry & Molecular Biology,
University of Alcalá, Spain.
Member of FEBS Education Committee

http://biomodel.uah.es/en/ (in English)
http://biomodel.uah.es/ (home page, in Spanish)

presentation,
course material

sample molecules
to practice

access to
mini-projects

Objectives

Introduction to the use of computer resources for locating and displaying (bio)molecular structure as 3D models.
Training in preparation of materials for support of teaching and learning, in the form of interactive displays and web pages.

Competences to acquire

Recognize and know existing resources that may be used as a support for teaching or to develop learning activities.
Discriminate the usefulness and applicability of each resource.
Use these resources for education.
Develop educational materials adapted to one’s particular needs.

Contents / Programme:

(time distribution is approximate, as we will adjust depending on how the course develops)

Hours	Monday, April 2^nd	Tuesday, April 3^rd	Wednesday, April 4^th
09:30 to 12:15	Demonstration of a selection of resources available in the internet and useful for understanding the three-dimensional structure and function of (bio)molecules. Protein Data Bank: macromolecules, link to other databases. PDB Molecule of the Month. PDB-101: Structural View of Biology Proteopedia: enriched information, personalised material. CACTUS NIH Chemical Identifier Resolver: chemical structures from their name Identification of other resources adequate for the needs of the attendees. Rules and plan for preparing your `mini-projects´.	Training in the use of Jmol software (continued) Some basic applied examples (continued) Identification of solutions adequate for the needs of the attendees. Some advanced applied examples: Distance-based actions: active centres, contacts… Procedure to store the resulting personalised models in order to display them in the classroom. Stand-alone files to be displayed in Jmol.	Procedure to store the resulting personalised models (continued) Further expansion and customisation (continued) Complete your project.
(--Lunch break--)
13:30 to 15:15	Training in the use of Jmol software as structure viewer and for preparation of structures to be displayed in the classroom. Some basic applied examples Rendering styles. The use of colour to convey information. Illustration of relevant regions in a molecule.	Complete the definition of your project. Procedure to store the resulting personalised models (continued) Web pages generated by Jmol. Further expansion and customisation of the web pages for a richer educational product. Basic webpage authoring practice.	Submit your project. Evaluation of the Course: “Mini-projects”
15:30 to 16:15	Discussion Start planning your project: find molecules write the 'story' you want to illustrate	Discussion Submit your project title. Build your project.	Conclusions
	Homework: think about your project, find molecules	Homework: work on building your project

Method

Multimedia presentation and work through examples with the attendees. Preparation of mini-projects.

Evaluation of the Course

Mini-projects will be given to the students and the student’s performance will be assessed.

Reference

http://wiki.jmol.org
How to use Jmol to study and present molecular structures. A. Herráez (2007) Lulu Enterprises: Morrisville, NC, USA. 144pp. ISBN 978-1-84799-259-8
+ Supplement 2011.

Use of molecular visualisation in the teaching practice Moleküler Görüntüleme Çalıştayı

Workshop (Course) Dokuz Eylül University, 2-3-4 April, 2012