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The practicals have several goals in this course. The main goal is to illustrate concepts that have been discussed in the seminars. The second goal is to exercise putative exam questions. And the third goal is that you get access to assistants so that you can ask questions. |
In the practicals we will focus on those aspects of the work discussed in the seminars that seem more difficult than others. The practicals will not cover all material, and thus be warned that you will also get exam questions about material that is not a topic in these practicals. The six seminars form a coherent series, and it often is an exam question to explain how the seminars together make one story. The questions in the practicals will help you with that. During the practicals you will occasionally get (very simple) questions about topics that will be discussed in a seminar that is still to come, and you will increasingly often get questions that require that you remebered what was discussed in the previous parts of the course.
The practicals will be protein structure centred. All protein structures you need are, of course, obtainable from the PDB, but as the PDB occasionally presents its users problems, we have cleaned-up and corrected the PDB files you need, and stored them in this website under the heading 'Exercise files', that you find in the window called 'Miscellaneous'.
Several small seminars and part of the practicals deal with amino acids. And some of the practicals even aim at familiarising you with the amino acids and their characteristics. These characteristics will not be part of the exam. The concepts related to hydrophobicity and the entropy of water, on the other hand, seem likely exam topics.
We will use YASARA for the practicals. Yasara is installed by CNCZ. Ask the assistants at the start of the first practical where YASARA can be found.
The answers to the questions in the practicals are hidden behind a password. At the end of each practical session the username and password to those answers will be replaced from something hard to guess to 'user' and 'geheim', respectively.
Feel free at any time to come to us at the CMBI with questions; also about practicals and seminars from a while ago.