Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)
If not done yet, please perform first the CYANA setup for the EMBO Practical Course on NMR in Garching (2019).
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.
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' (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
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 use the same demo in the 'demoquick/auto' directory, which speeds up the calculation by setting 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=25; CALC" | tee CALC.out
In this example, the structure calculations will be performed using 25 processors in parallel. The screen output is kept in the file 'CALC.out'. Alternatively, you can run the calculation completely in the background:
cyana "nproc=25; 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.
You can visualize the structure bundle, for example, with MOLMOL. To automatically superimpose the structures in MOLMOL, give it the appropriate residue range(s):
molmol -r 8-43,48-109 final.pdb
Alternatively, you can use the program YASARA, started by typing 'yasara' at the Linux prompt. Or, you use PyMOL on the Windows machine (use FileZilla in Windows to transfer files between Linux and Windows).