Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)

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CYANA setup for the EMBO Practical Course on NMR in Garching (2019)

If not done yet, please follow the following steps:

  1. Log in to the Windows computer.
  2. Start 'nx' to log in to one of the three Linux clusters, cluster01, cluster02, cluster03.
  3. Go to your home directory.
  4. Make a new directory for the practical.
  5. Copy the input data for the practical.

Linux commands for steps 3-5 (you may copy them into a terminal): 

cd ~
mkdir CYANA
cd CYANA
cp -a /ms/data/prog/cyana/current/demo* .

There will be four demo directories with example data for the practical:

  • demo: Input data for the standard denos
  • demoquick: Input for the same demos, but modified for quick calculation (at some expense of quality)
  • demo-results: Input data and results for the standard demos
  • demoquick-results: the same for the "quick" demos

The program CYANA can be started by typing its name, 'cyana', and quit by typing 'quit' or 'q': 

cd demoquick/basic
cyana
___________________________________________________________________

CYANA 3.98.12 (intel)

Copyright (c) 2002-18 Peter Guentert. All rights reserved.
___________________________________________________________________

    Time-limited license valid until 2019-12-31.
    Library file "/home/guentert/src/cyana-3.98.12/lib/cyana.lib" read, 41 residue types.
    Sequence file "demo.seq" read, 114 residues.
cyana> q

If all worked, you are ready to go!

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.

Basic structure calculation with given restraints

The basic type of structure calculation with CYANA uses already prepared input restraint files. An example is in the 'demo/basic' (or 'demoquick/basic') directory.

Refer to the description here to perform the structure calculation.

Structure calculation using assigned NOESY peak lists

CYANA can convert assigned NOESY peak lists into distance restraints, and perform a structure calculation with these (and possibly other types of restraints). An example is in the 'demo/manual' (or 'demoquick/manual' for a faster version) directory.

Refer to the description here to perform the structure calculation.

Combined automated NOESY assignment and structure calculation

Refer to the description here to perform automated NOESY assignment and structure calculation.


Automated NOE restraint assignment and the structure calculation by torsion angle dynamics is included in 'CALCstructcalc.cya' (see above).

Alternatively, you can also perform automated NOE restraint assignment and the structure calculation separately with the 'CALCauto.cya' macro. The 'flya.prot' file from the automated resonance assignment (e.g. with 'CALC.cya'; backbone and side-chain assignments are required!) will be used together with the (unassigned) NOESY peak lists to assign the NOESY peaks and to generate distance restraints in order to compute the three-dimensional structure of the protein.

TALOS-N can be used to generate torsion angle restraints from the backbone chemical shifts in 'flya.prot'. To do this, use the CYANA commands 

read flya.prot
talos
write talos.aco

This will call the program TALOS-N and store the resulting torsion angle restraints in the file 'talos.aco'.

For further information about automated NOESY assignment you can consult the Tutorial Structure calculation with automated NOESY assignment (which uses different file names than we have here).

To speed up the calculation, you can set in 'CALCauto.cya': 

structures:=50,10
steps=5000

These commands tell the program to calculate, in each cycle, 50 conformers, and to analyze the best 10 of them. 5000 torsion angle dynamics steps will be applied per conformer.

Seven cycles of automated NOE assignment and structure calculation will be performed by running the command 

cyana "nproc=25; CALC"

Statistics on the NOE assignment and the structure calculation can be obtained with the command 'cyanatable -l'.

The final structure will be 'final.pdb'. The optimal residue range for superposition can be found with the command 

cyana overlay final.pdb

or with the CYRANGE web server.

You can visualize the structure bundle, for example, with PyMOL. To superimpose the structures in PyMOL, you can use the internal PYMOL command with the appropriate residue range: 

intra_fit resi 8-110
set all_states
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