In this tutorial we will

1. determine how to calibrate NOE data to obtain distance restraints,
2. derive a ligand bio-active conformation with the software CYANA,
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)

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.

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

Remark: CYANA is a proprietary software. For any installation problem, contact Peter Güntert, the the author of CYANA.

Molecular viewer  

You need also a molecular viewer capable of saving mol2 file

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

NMR² 

NMR² runs via the platform SAMSON.

1. Register and install SAMSON
2. Request the NMR² application

solutions