Setting the Parameter File

The parameter file (‘parameters.txt’) is a text file that should be located at the directory that you are running ADAPT-NMR. It includes all the information that ADAPT-NMR needs from the user.

Most of the parameters have been optimized for a typical protein and do not need to be modified in most cases. However, there are required parameters (Number of Amino Acids, Sequence File, and sequqnce_letter) that need to be set by the user at each run.

The following table describes all the parameters in the file and indicates if any modification is required or suggested. We suggest no modification to the values flagged as “Optimized” unless if you are unhappy with the final result. You can always change those parameters after a full run of ADAPT-NMR and the result will be updated accordingly.

Parameter	Default Value	Acceptable Values	Modification Suggestion	Description
n_residue	N/A	Any	required	Number of Amino Acids in the proteoin
sequence_file	N/A	Relative address of the sequence file	required	The sequence of the protein in the three letter or the one letter format
sequence_letter	N/A	3 or 1	required	Describes whether the sequence file you provided (sequence_file) is in the three letter or the one letter format
hcconh_peak_list_file	0	Relative address of the peak list file	Optional	This is an optional input if you want to include 3D HBHA(CO)NH peak list in the analysis and the assignment process. The file should be in sparky format.
cconh_peak_list_file	0	Relative address of the peak list file	Optional	This is an optional input if you want to include 3D H(CCO)NH peak list in the analysis and the assignment process. The file should be in sparky format.
hcch_tocsy_peak_list_file	0	Relative address of the peak list file	Optional	This is an optional input if you want to include 3D HCCH-TOCSY peak list in the analysis and the assignment process. The file should be in sparky format.
hbhaconh_peak_list_file	0	Relative address of the peak list file	Optional	This is an optional input if you want to include 3D HBHA(CO)NH peak list in the analysis and the assignment process. The file should be in sparky format.
assignment_level	0.95	0-1	Optimized	One of the stopping criteria’s for data collection. The default value is set to reach to at least 95% of completeness in the assignment.
window_size_peak_picking	2	1-5	Optimized	A parameter in the peak picking algorithm. By setting the default value as two, it recognize a data point as a Local Maximum if its height is higher than two adjacent data point in any direction.
min_peak_distance	3	1-5	Optimized	Another parameter in the peak picking algorithm. If a peak is less than ‘min_peak_distance’ data point away from a larger peak it should satisfy other requirement to be recognized as a peak. It has been optimized to minimize the noise artifact.
max_1d_aligning_shift	3	1-10	Optimized	A parameter in the alignment algorithm that determines the maximum allowed shift across tilted planes.
max_hsqc_peaks	1.3	Any	Optimized	One of the criteria in peak picking the HSQC spectrum is the number of amino acids in the sequence of the protein. This parameter sets the upper limits for the ratio of the number of peaks divided by the number of amino acids.
min_hsqc_peaks	1.1	Any	Optimized	This parameter sets the lower limits for the ratio of the number of peaks divided by the number of amino acids in HSQC spectrum.
xsens_disp	3	1-10	Optimized	A parameter in the dispersion function calculation that defines the ideal dispersion. Two peaks are considered dispersed in the direct dimension if they are more than ‘xsens_disp’ data point away in the direct dimension.
ysens_disp	3	1-10	Optimized	Two peaks are considered dispersed in the indirect dimension if they are more than ‘ysens_disp’ data point away in the direct dimension.
water_centered_flg	0	0 or 1	Optional