Basic structure calculation starting from given restraints: Difference between revisions
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When CYANA is started, it automatically | When CYANA is started, it automatically executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the '''init.cya''' file: | ||
rmsdrange:=10-100 # define residue range for RMSD calculations | rmsdrange:=10-100 # define residue range for RMSD calculations | ||
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read seq demo.seq # read amino acid sequence | read seq demo.seq # read amino acid sequence | ||
The actual structure calculation is performed by the commands in the macro file CALC.cya: | The actual structure calculation is performed by the commands in the macro file '''CALC.cya''': | ||
read upl demo.upl # read upper distance bounds | read upl demo.upl # read upper distance bounds | ||
Revision as of 11:35, 2 June 2009
This calculation shows how to calculate a structure from previously assigned upper limits. The input data are in the subdirectory ‘basic’ of the demo data zip archive:
- demo.seq
- amino acid sequence
- demo.upl
- upper distance limit restraints
- demo.aco
- dihedral angle restraints
- init.cya
- initialization macro
- CALC.cya
- macro for the structure calculation
When CYANA is started, it automatically executes the commands in the initialization macro file init.cya, which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the CALC.cya macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the init.cya file:
rmsdrange:=10-100 # define residue range for RMSD calculations cyanalib # read standard CYANA residue library read seq demo.seq # read amino acid sequence
The actual structure calculation is performed by the commands in the macro file CALC.cya:
read upl demo.upl # read upper distance bounds read aco demo.aco # read dihedral angle restraints calc_all 50 steps=4000 # calculate conformers overview demo.ovw structures=10 pdb # analyze and write best conformers