Basic structure calculation starting from given restraints: Difference between revisions
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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: | 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 looks for the 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 CALC.cya (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. | When CYANA is started, it automatically looks for the 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 CALC.cya (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. | ||
Revision as of 12:21, 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 looks for the 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 CALC.cya (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.
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