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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, NMR2, and excel (or similar)



Content

  • Software

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 (to come data.zip)
  3. Unpack the input data for the practical
  4. Get the demo version of CYANA for this practical (or here CYANA webpage)
  5. Unpack CYANA
  6. Go to the downloaded CYANA folder
  7. Test whether CYANA can be started by typing, './cyana'
  8. If you are a mac user you may need to remove the safety quarantine
  9. Setup the CYANA environment variables
  10. Go to the newly created directory 'data'
  11. Test whether CYANA can be started by typing its name, 'cyana'
  12. Exit from CYANA by typing 'q' or 'quit'

cd "download path"/cyana-3.98.15 
#optional 
sudo xattr -rd com.apple.quarantine cyanaexe.macarm-gfortran
./cyana   

CYANA 3.98.15 (macarm-gfortran)

Copyright (c) 2002-22 Peter Guentert. All rights reserved.
___________________________________________________________________

    Demo license valid for specific sequences until 2024-12-31.

    Library file "/Users/julienorts/Downloads/cyana-3.98.15/lib/cyana.lib" read, 41 residue types.



cd data
cyana

___________________________________________________________________

CYANA 3.98.15 (macarm-gfortran)

Copyright (c) 2002-22 Peter Guentert. All rights reserved.
___________________________________________________________________

    Demo license valid for specific sequences until 2024-12-31.

    Library file "/Applications/demo-cyana-3.98.15/lib/cyana.lib" read, 41 residue types.
*** ERROR: Illegal residue name "MOL".
*** ERROR: Cannot read line 113:
           MOL  999

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.

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

Molecular viewer  

You need also a molecular viewer capable of saving mol2 file

  1. Download Chimera (to your personal laptop) from: Chimera


solutions