Usage
Run CS-GAMDy with a command:
python gamdy_current.py -cs PATH_TO_FILE_WITH_CHEMICAL_SHIFTS -f PATH_TO_FILE_WITH_STARTING_STRUCTURE -ss PATH_TO_FILE_WITH_SECONDARY_STRUCTURE -dih_dir PATH_TO_DIRECTORY_WITH_TODIHEDRAL_ANGLE_RESTRAINTS -rgyr_value RADIUS_OF_GYRATION -rgyr_res START_RESIDUE:END_RESIDUE
Example with input files included with CS-GAMDy distribution :
python gamdy_current.py -cs Ubiquitin.corr -f unfolding2_sa1_60_3A.pdb -ss 1UBQ_TalosN_SS_talos_ss.txt -dih_dir 1UBQ_TNb1STD -rgyr_value 11 -rgyr_res 2:72
Explanation of arguments:
"-cs" - path to a file with chemical shifts in NMR-STAR 2.1 format.
Parameter PATH_TO_FILE_WITH_CHEMICAL_SHIFTS should be a string.
"-f" - path to a file with coordinates of the starting model in the PDB format.
Parameter PATH_TO_FILE_WITH_STARTING_STRUCTURE should be a string.
"-ss" - path to a file with secondary structure derived from chemical shifts.
Parameter PATH_TO_FILE_WITH_SECONDARY_STRUCTURE should be a string.
"-dih_dir" - path to a directory with torsion angle restraints in XPLOR format.
Parameter PATH_TO_DIRECTORY_WITH_DIHEDRAL_ANGLE_RESTRAINTS should be string.
"-rgyr_res" - first and last residues of a protein region that should be used in calculations of radius of gyration. A good strategy is to exclude N- and C-termini with S2 < 0.7 (as reported by the backbone RCI webserver).
Parameters START_RESIDUE and END_RESIDUE should be numbers (integers). In the example above, START_RESIDUE = 2 and END_RESIDUE = 72.
"-rgyr_value" - radius of gyration for these residues under an assumption of a globular structure (see equation at http://nmr.cit.nih.gov/xplor-nih/xplorMan/node412.html).
Parameter RADIUS_OF_GYRATION should be a a number (float)
|
|
Problems? Suggestions? Please
contact Wishart group
|
