View source for Structure calculation with automated NOESY assignment

← Structure calculation with automated NOESY assignment

You do not have permission to edit this page, for the following reason:

The action you have requested is limited to users in the group: Users.

You can view and copy the source of this page.

This calculation shows how to calculate a structure from previously unassigned NOESY peak lists. The input data are in the subdirectory ‘demo/auto’ of the CYANA software package:

;demo.seq:amino acid sequence
;c13.peaks:peak list from 3D <sup>13</sup>C-resolved NOESY spectrum
;n15.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum
;aro.peaks:peak list from 3D aromatic <sup>13</sup>C-resolved NOESY spectrum
;demo.prot:<sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N chemical shift list
;demo.aco:dihedral angle restraints
;CALC.cya:macro for the structure calculation


Combined automated NOESY cross peak assignment and structure calculation are performed with the macro file '''CALC.cya''':

 peaks       := c13.peaks, n15.peaks, aro.peaks # NOESY peak lists in XEASY format
 prot        := demo.prot                       # names of chemical shift list(s)
 restraints  := demo.aco                        # additional (non-NOE) restraints
 tolerance   := 0.04, 0.03, 0.45                # shift tolerances: H, H', C/N', C/N
 #calibration_constant:=6.7E5,8.2E5,8.0E4       # calibration constants, automatic if empty
 structures  := 100,20                          # number of initial, final structures
 steps       := 10000                           # number of torsion angle dynamics steps
 randomseed  := 434726                          # random number generator seed
 
 noeassign peaks="$peaks" prot="$prot" autoaco

First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.



[[Image:StructuresDemoManual.png|thumb|200px|'''demo.pdb''']]
Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.*''', '''cycle2.*''', etc.

An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

Return to Structure calculation with automated NOESY assignment.

Retrieved from "https://cyana.org/wiki/Structure_calculation_with_automated_NOESY_assignment"

View source for Structure calculation with automated NOESY assignment

Navigation menu

Search