Structure calculation using manually assigned NOESY peak lists: Difference between revisions
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overview $name.ovw structures=20 pdb # write overview file and coordinates | overview $name.ovw structures=20 pdb # write overview file and coordinates | ||
First several variables are set: The variable '''name''' is used to define the name of various input and output files. 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 [[ | First several variables are set: The variable '''name''' is used to define the name of various input and output files. 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 [[tolerance]] specifies | ||
The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''. | The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''. |
Revision as of 21:32, 2 June 2009
This calculation shows how to calculate a structure from previously assigned NOESY peak lists. The input data are in the subdirectory ‘manual’ of the demo data zip archive:
- demo.seq
- amino acid sequence
- c13.peaks
- peak list from 3D 13C-resolved NOESY spectrum
- n15.peaks
- peak list from 3D 15N-resolved NOESY spectrum
- aro.peaks
- peak list from 3D aromatic 13N-resolved NOESY spectrum
- demo.prot
- 1H, 13C, and 15N chemical shift list
- demo.aco
- dihedral angle restraints
- init.cya
- initialization macro
- CALC.cya
- macro for the structure calculation
The structure calculation is performed by the commands in the macro file CALC.cya:
name := demo peaks := c13,n15,aro # names of peak list(s) prot := $name # names of proton list(s) tolerance := 0.040,0.030,0.45 # shift tolerances: H, H', C/N', C/N calibration:= 6.7E5,8.2E5,8.0E4 # calibration constants, automatic if empty dref := 4.2 # average distance limit for automatic calibration if (master) then # execute the following commands only on master node # ---- check consistency of peak and chemical shift lists---- peakcheck peaks=$peaks prot=$prot # check consistency of peak and shift assignments # ---- calibration ---- calibration prot=$prot peaks=$peaks constant=$val('calibration') dref=$dref # calibrate NOEs peaks calibrate "**" simple # convert calibrated NOEs into distance restraints write upl $name-in.upl # write initial upper distance limit file distance modify # remove irrelevant restraints, apply pseudoatom corrections write upl $name.upl # write upper distance limit file end if synchronize # wait until all parallel processes have arrived here # ---- structure calculation ---- read seq $name.seq # re-read sequence to initialize read upl $name.upl # read upper distance limits read aco $name.aco # read angle restraints seed=5671 # set random number generator seed calc_all structures=100 command=anneal steps=10000 # calculate conformers overview $name.ovw structures=20 pdb # write overview file and coordinates
First several variables are set: The variable name is used to define the name of various input and output files. 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 tolerance specifies The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard simulated annealing schedule with 4000 torsion angle dynamics steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file demo.ovw, and their coordinates are written to the PDB file demo.pdb.