Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021): Difference between revisions

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== Basic structure calculation with given restraints ==
== 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.  
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 [[Basic structure calculation starting from given restraints|here]] to perform the structure calculation.
Refer to the description [[Basic structure calculation starting from given restraints|here]] to perform the structure calculation.
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== Structure calculation using assigned NOESY peak lists ==
== 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.  
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 [[Structure calculation using manually assigned NOESY peak lists|here]] to perform the structure calculation.
Refer to the description [[Structure calculation using manually assigned NOESY peak lists|here]] to perform the structure calculation.
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* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]
* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]


<!--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.
To speed up the calculation, you can set in the 'CALC.cya' macro:
 
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 use the same demo in the 'demoquick/auto' directory, which speeds up the calculation by setting in the 'CALC.cya' macro:


  structures:=50,10
  structures:=50,10
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Seven cycles of automated NOE assignment and structure calculation will be performed by running the command
Seven cycles of automated NOE assignment and structure calculation will be performed by running the command


  cyana "nproc=25; CALC" | tee CALC.out
  cyana "nproc=10; 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:
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=25; CALC" > CALC.out &
  cyana "nproc=10; CALC" > CALC.out &


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


or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].
or with the [http://www.bpc.uni-frankfurt.de/cyrange.html 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).


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:
== Results ==


intra_fit resi 8-110
You can download the [http://www.cyana.org/demo-results.tgz results of all CYANA demo calculations] (92 MB).
set all_states
-->

Latest revision as of 10:52, 28 September 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:

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).

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