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)


Your guide in this course:

Prof. Angel Herráez
Dep. Biochemistry & Molecular Biology,
University of Alcalá, Spain.
Member of FEBS Education Committee (in English) (home page, in Spanish)


Competences to acquire

Contents / Programme:

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


Monday, April 2nd

Tuesday, April 3rd

Wednesday, April 4th



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--)


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”



Start planning your project:

  • find molecules
  • write the 'story' you want to illustrate


Submit your project title.

Build your project.



  Homework: think about your project, find molecules Homework: work on building your project  


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.