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In this tutorial we will

  1. determine how to calibrate NOE data to obtain distance restraints,
  2. derive a ligand bio-active conformation,
  3. introduce the NMR2 approach for protein-ligand 3D structure elucidation.


To this end we will use the software CYANA and  NMR2. 



Content

  • CYANA setup

CYANA setup 

Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):

  1. Go to your home directory (or data directory).
  2. Get the data for the practical from the server (data.zip).
  3. Unpack the input data for the practical.
  4. Get the demo version of CYANA for this practical.
  5. Unpack CYANA.
  6. Setup the CYANA environment variables.
  7. Change into the newly created directory 'data'.
  8. Copy the demo_data directory to 'flyabb'.
  9. Change into the subdirectory 'flyabb'.
  10. Test whether CYANA can be started by typing its name, 'cyana'.
  11. Exit from CYANA by typing 'q' or 'quit'.
  12. Download Chimera (to your personal laptop) from: Chimera
  13. Download Avogadro (to your personal laptop) from: Avogadro
cd data
cp -r demo_data flyabb 
cd flyabb




cyana
___________________________________________________________________

CYANA 3.98 (mac-intel)

Copyright (c) 2002-17 Peter Guentert. All rights reserved.
___________________________________________________________________

    Demo license valid for specific sequences until 2018-12-31

    Library file "/Users/deans/cyana-3.98/lib/cyana.lib" read, 41 residue types.
*** ERROR: Illegal residue name "LIG".
*** ERROR: Cannot read line 114:
           LIG  333
cyana> q

If all worked, you are ready to go in terms of everything related to CYANA! The reason you see the ERROR message, is because you have a sequence file in the directory, but not a library file for the ligand yet. Don't worry, this is as expected and you will take care of it during the exercise.

If you want to return to your practical later, using your own Linux or Mac OS X computer, you can download the demo version of CYANA from here.

Hint: More information on the CYANA commands etc. is in the CYANA 3.0 Reference Manual.


solutions