Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)

Installation of CYANA demo version

If not done yet, please install the demo version of CYANA.

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' directory of the CYANA package.

Refer to the description here to perform the structure calculation.

Variants of this basic structure calculation that include other types of input data are in the directories 'demo/rdc' (with residual dipolar couplings), 'demo/pcs' (pseudocontact shifts), 'demo/dimer' (homodimer symmetry restraints), and 'demo/rna' (RNA).

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' directory.

Refer to the description here to perform the structure calculation.

Combined automated NOESY assignment and structure calculation

CYANA can automatically assign NOESY peak lists and calculate a structure in an iterative protocol comprising seven cycles of combined automated NOESY asssignment and structure calculation.

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

The protocol is described in complete detail in the following publication:

• Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453-471 (2015)

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

structures:=50,10
steps=5000

These commands tell the program to calculate, in each cycle, 50 conformers (instead of the standard of 100), and to analyze the best 10 (instead of 20) of them. 5000 (instead of 10000) 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=10; CALC" | tee CALC.out

In this example, the structure calculations will be performed using 10 processors (if available!) in parallel. The number of processors should not be larger than the number of structures to calculate. The screen output is kept in the file 'CALC.out'. Alternatively, you can run the calculation completely in the background:

cyana "nproc=10; CALC" > CALC.out &

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.

Results

You can download the results of all CYANA demo calculations (92 MB).