These use cases describe how to run CYANA 3.0 jobs on the eNMR grid.
Gzipped tar files containing all the necessary files and an example of a job file for grid submission are provided for download. These use cases provide a basis for executing any CYANA 3.0 job on the eNMR grid.
Description of content:
These directories contain examples for structure calculation with CYANA 3.0
Created by Peter Güntert / Henry Jonker, BMRZ, November 2008
General input and jobsubmission files:
- cyana.jdl : job file for grid submission, modify path as needed
- cyana.run : executable script that will run the CYANA program
- CALC.cya or AUTO.cya : macro to execute the CYANA calculation
- init.cya : initial input parameters for CYANA
Basic structure calculation: (file: usecase_cyana_basic.tgz)
This is a basic example of a CYANA structure calculation from given conformational restraints. It is assumed that NOEs have already been assigned and converted to upper distance bounds. No automated assignment of NOEs is performed.
Basic input files:
- demo.seq : protein sequence
- demo.aco : dihedral angle restraints
- demo.upl : upper distance bounds
Basic output files:
- demo.ovw : structure and violation statistics
- demo.pdb : structure bundle
CYANA with manual NOESY assignment: (file: usecase_cyana_manual.tgz)
This is an example for a CYANA structure calculation using manual NOESY peak assignments. The input data are the protein sequence, assigned NOESY peak lists in XEASY format, a chemical shift list and a dihedral angle restraints list. The NOE distance bounds are calibrated by CYANA (output-file: demo-in.upl).
CYANA with automated NOESY assignment: (file: usecase_cyana_auto.tgz)
This is an example for a complete CYANA structure calculation using automated NOESY assignment. The input data are unassigned NOESY peak lists in the format of the program XEASY or NMRView and a chemical shift list.
Input files:
- aro.peaks, c13.peaks, n15.peaks : NOESY peak lists (in XEASY format)
- aro.xpk, c13.xpk, n15.xpk : NOESY peak lists (in NMRView format)
- demo.prot : chemical shift list
Output files:
- cycle(1-7).ovw, final.ovw : structure and violation statistics
- cycle(1-7).pdb, final.pdb : structure bundles
- cycle(1-7).noa : detailed automated NOESY assignment information
- cycle.aco, final.aco : torsion angles for the Ramachandran plot and staggered rotamers
- cycle0.upl : list of covalently restrained short distances
- cycle(1-7).upl, final.upl : NOE upper distance bounds
- (aro/n15/c13)-cycle7.peaks : assigned NOESY peak list in XEASY format
- (aro/n15/c13)-cycle7-ref.peaks : color-coded peak list with input assignments
- demo-final.prot : chemical shift list with optimally swapped diastereotopic pairs
- finalstereo.cya : tentative stereospecific assignments for the final structure calculation
- rama.ps : Ramachandran plot in postscript format for the final structure calculation
CYANA structure calculation of a homodimer: (file: usecase_cyana_dimer.tgz)
This is an example for a CYANA structure calculation of a homodimer using automated NOESY assignment. The input data are the protein sequence, unassigned NOESY peak lists in XEASY format, a chemical shift list and dihedral angle restraints.
CYANA with residual dipolar couplings: (file: usecase_cyana_rdc.tgz)
This use case contains examples for CYANA structure calculations with residual dipolar couplings (RDCs). The input data are the protein sequence a chemical shift list, residual dipolar coupling restraints (input file: demo.rdc) and dihedral angle restraints with either unassigned NOESY peak lists in XEASY format (auto) or callibrated NOE distance restraints (manual). An example (macro: FindTensor.cya) is included to find the allignment tensor magnitude and rhombicity values.
CYANA with pseudocontact shift restraints: (file: usecase_cyana_pcs.tgz)
This is an example for a CYANA structure calculation using pseudocontact shifts (PCSs) restraints. The input data are the protein sequence, upper distance bounds, pseudocontact shift restraints (input files: demo.pcs, pcs.upl) and dihedral angle restraints.
Execution on the eNMR grid: (commands are in italics)
1) Login as an eNMR grid user:
voms-proxy-init -voms enmr.eu
2) Submit job file:
glite-wms-job-submit -o cyana.jobid -a cyana.jdl
3) Check status:
glite-wms-job-status -i cyana.jobid
4) When finished get back output:
glite-wms-job-output -i cyana.jobid --dir cyana-output