WHAT IF Course

The WHAT IF user and molecular modelling course will be organized once a year. This course is intended for novices in the protein modelling field who intend to use WHAT IF as their modelling and graphics package.

The WHAT IF course is a one week course which starts on Monday at 13.00. The course room will be open/available already Monday at 11:00 (to read your Email etc). We will have practical work with excercises and also some lectures in between every day from 10:00 to 18:00 except Wednesday when we will stop at 16:00 for some social events. The course will end Friday afternoon around 15:00. The location is our course room, at CMBI, at the ground floor of the NCMLS

Teachers:  Robbie Joosten, Gert Vriend
Max. number of participants: 18

The material for all our courses is a available.

Participating

WHAT IF courses are free of cost. Participants have to count, however, with a hotel bill (if a hotel is needed) and of course they have to pay for their travel and food. Look here for CMBI Directions and Hotel information

Registration

Please register by sending an email to Barbara van Kampen .

Course contents

This course consists of two parts:

  • Short informal seminars about the theory behind WHAT IF options.
  • Long practical WHAT IF usage sessions.

A detailed time schedule is available, but this schedule can only be indicative as it all determines on the skills and enthusiasme of the participants.

Seminars

The following seminars are routinely given (additional seminars can be added upon request):

  • Molecular graphics and molecular modelling software.
  • Model building by homology.
  • Protein structure and protein model verification.
  • Energy minimizations and molecular dynamics.
  • Secondary structure prediction.

Preparations

There are no specific preparations needed for the course. However, if you want to look at one specific molecule on the last day of the course, you should make sure that that molecule is already here before the course. So, contact Gert Vriend long enough before the course to have Gert check that it is readable.

Please be aware that this is a WHAT IF user course. We assume that you already know homology modelling theory etc., and will only teach you how to do such things with WHAT IF. But at the end you can really do everything with the software you want.

 

Detailed course program

 

Obviously, there is no way that we are going to follow the program listed below. The course is interactive. With experienced modelers we will go much faster, and with novices much slower. But just in case your boss wants to see a program before he frees up the money for the ticket, here it is.The WHAT IF course knows four kinds of sessions:

  • Practical training sessions.
    In these sessions the participants get many of the WHAT IF options explained. This mostly happens by typing commands from example scripts and discussing the commands and the outcome with a course teacher.
  • Question sessions.
    These are just what the word indicates, sessions where we sit around the table, all teachers are available, and you can ask your questions.
  • Exercise sessions.
    In these sessions the participants will answer questions using WHAT IF, but ready to type answers are not available, so the user really has to use (and deepen) his/her knowledge of the software.
  • Research sessions.
    These are meant to see if you can already work on your own in-house research using WHAT IF.
At regular intervals the sessions will be interrupted for short seminars that explain very briefly the ideas behind WHAT IF options (i.e. hydrogen bonds, accessible surface, Ramachandran plot, the proprietary databases, structure validation, homology modelling). These are not extensive scientific seminars, but short, quick explanations of how the underlying theory is implemented in WHAT IF.
Monday    
13:00 - 14:00 Welcome, practical things, Introduction to WHAT IF usage.
14:00 - 15:30 Practical WHAT IF training session
15:30 - 16:00 Tea and question session
16:00 - 17:30 Practical WHAT IF training session

Tuesday
10:00 - 11:00 Practical WHAT IF training session
11:00 - 11:30 Coffee and question session
11:30 - 12:30 Practical WHAT IF training session
12:30 - 13:30 Lunch
13:30 - 15:30 Practical WHAT IF training session
15:30 - 16:00 Tea and question session
16:00 - 17:30 Practical WHAT IF training session

Wednesday 10:00 - 11:00 Practical WHAT IF training session
11:00 - 11:30 Coffee and question session
11:30 - 12:30 Practical WHAT IF training session
12:30 - 13:30 Lunch
13:30 - 15:30 Exercise session
15:30 Tea and departure for 'social event'

Thursday
10:00 - 11:00 Exercise session
11:00 - 11:30 Coffee and question session
11:30 - 12:30 Exercise session
12:30 - 13:30 Lunch
13:30 - 15:30 Exercise session
15:30 - 16:00 Tea and question session
16:00 - 17:30 Exercise session

Friday
10:00 - 11:00 Exercise session
11:00 - 11:30 Coffee and question session
11:30 - 12:30 Exercise session
12:30 - 13:30 Lunch
13:30 - 15:30 Exercise session
15:30 Tea and departure