Structure calculation and automated NOESY assignment with CYANA (EMBO 2019): Difference between revisions
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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. | ||
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 == | == Structure calculation using assigned NOESY peak lists == | ||
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== Combined automated NOESY assignment and 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 [[Structure calculation with automated NOESY assignment|here]] to perform automated NOESY assignment and structure calculation. | Refer to the description [[Structure calculation with automated NOESY assignment|here]] to perform automated NOESY assignment and structure calculation. | ||
<!--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. | |||
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 | 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 | ||
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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). | 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). | ||
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To speed up the calculation, you can | To speed up the calculation, you can use the same demo in the 'demoquick/auto', which speeds up the calculation by setting in the 'CALC.cya' macro: | ||
structures:=50,10 | structures:=50,10 | ||
steps=5000 | 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. | 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 | Seven cycles of automated NOE assignment and structure calculation will be performed by running the command | ||
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cyana "nproc=25; CALC" | cyana "nproc=25; CALC" | ||
In this example, the structure calculations will be performed using 25 processors in parallel. If you want to keep the screen output of the calculation in a file, 'CALC.out', you may replace the preceding command with | |||
cyana "nproc=25; CALC" | tee 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'. | ||
Revision as of 15:51, 28 July 2019
CYANA setup for the EMBO Practical Course on NMR in Garching (2019)
If not done yet, please follow the following steps:
- Log in to the Windows computer.
- Start 'nx' to log in "your" Linux server.
- From "your" Linux server, log in to one of the three Linux clusters, cluster01, cluster02, or cluster03.
- Go to your home directory.
- Make a new directory 'CYANA' for the practical.
- Copy the input data for the practical.
Linux commands for steps 3-6 (you may copy them into a terminal):
ssh -Y cluster02.nmr.ch.tum.de) 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 demos
- 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.
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.
To speed up the calculation, you can use the same demo in the 'demoquick/auto', 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"
In this example, the structure calculations will be performed using 25 processors in parallel. If you want to keep the screen output of the calculation in a file, 'CALC.out', you may replace the preceding command with
cyana "nproc=25; CALC" | tee 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:
molmol -r 8-110 final.pdb
Alternatively, you can use the program YASARA. Start it with the command 'yasara'.