In this tutorial we will
- determine how to calibrate NOE data to obtain distance restraints,
- derive a ligand bio-active conformation with the software CYANA,
- 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
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CYANA Setup
Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):
- Go to your home directory (or data directory)
- Get the data for the practical from the server (to come data.zip)
- Unpack the input data for the practical
- Get the demo version of CYANA for this practical (or here CYANA webpage)
- Unpack CYANA
- Go to the downloaded CYANA folder
- Test whether CYANA can be started by typing, './cyana'
- If you are a mac user you may need to remove the safety quarantine
- Setup the CYANA environment variables
- Go to the newly created directory 'data'
- Test whether CYANA can be started by typing its name, 'cyana'
- 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
- Download Chimera (to your personal laptop) from: Chimera
NMR2
NMR2 runs via the platform SAMSON.
- Register and install SAMSON
- Request the NMR2 application