6CYANA: spec pick contour - CYANA command

Parameters: method=nodiag|diag             (default: diag)
            scale=<float list>             (required)
            contourdim=<string list>       (required)
            peakarea=<integer>             (default: 7)
            basefactor=<real>              (default: 3.0)
            factor=<real>                  (default: 1.3)
            userglobal=<real>              (optional)
            pickrange=<float list>         (default: minimal and maximal chemical shifts)
            sol=<string list>              (optional)
            waterline=<float list>         (default: 4.7 in each H dimension)
            watertol=<float list>          (default: 0.04)
            only_pos                       (option)
            only_neg                       (option)
            half_pixel_cal                 (option)
            include_diagonal               (option)
            diagnoal_tol=<float>           (optional,default:0.2)

Performes peak picking using the CYANA contour line analysis approach

<method> specifies the condition for local extremum determination.
Provided modes are 'diag' (all neighbors of a data point are
considered) and 'nodiag' (only direct neighbors of a data point
are considered).

<scale> is used to specify the scaling factor of the spectral axes.
The individual scaling factors have to be provided in the same
order as in the <format> specification (see read spectrum).
Individual values are separated by ``,'', e.g. scale=0.03,0.03,0,4
Scaling factor equals the peak width at half height.

<contourdim> defines the 2D plane to be analyzed. Contour lines
can only be created in 2D.  Dimensions for which contour lines
should be created have to be provided by the user following the
CYANA library nomenclature, e.g. contourdim=HC,C

<peakarea> defines the size of the box in each dimension around
a local maximum within which contour lines are created and analyzed.
The size of <peakarea> can be provided by the user. Smaller values
lead to a faster scanning of the spectrum. For  peak picking it
is vital to choose a sufficiently large '<peakarea> otherwise it
does not influence the outcome of the algorithm.

<basefactor> is a multiplication factor for the noise level to give
the intensity of the first contour line.

<factor> is a multiplication factor for determining the intensity
of the next higher contour line by multiplying with the intensity of
current contour line.

<userglobal>: instead of calculating the global noise level using the
CYANA command <spec noise> the user can set the noise level explicitly.

<pickrange> specifies the spectral range in ppm that is to be picked. Ranges
belonging to different dimensions can be separated by ``,''. The order of
the ranges specified has to correspond to the order of the dimensions
given in <format>, e.g. pickrange=1.0..10.0, 2.0..11.0,0.0..75.0. If one wants
to select the complete spectral range in for example dimension 1, one can
write: pickrange=,2.0..11.0,0.0..75.0.

If the option <only_pos> is given only positive signals are considered, else if
the option <only_neg> is given only negative signals are considered. If
none of these two options set, both negative and positive signals are included
in the analysis.

There are two ways of interpreting the maximal chemical shift of the spectrum,
usually given in ppm: (i) interpreting the chemical shift as ppm of the edge
of the spectrum, i.e. the left side of the left pixel, or (ii) the center of the
first pixel.  If the option 'half_pixel_cal' is set, the maximal chemical shift
is construed as explained in (ii).

<sol> specifies dimension(s) that has(have) a solvent signal which is to be excluded.
The axis label has to follow the nomenclature of the 'format' specification,
e.g. sol=HC,H. The order is irrelevant in this case.

<waterline> determines the region of the solvent signal to be excluded in ppm.
Different positions can be indicated for varying dimensions but have to follow
the order given in <sol>, e.g. waterline=4.7,4.6

<watertol> represents the tolerance range for solvent region to be excluded in
ppm, i.e.<waterline> +- <watertol>. Different tolerances can be indicated for
varying dimensions but have to follow the order given in 'sol',
e.g. waterline=0.5,0.3

If the option <include_diagonal> is set diagonal peaks of corresponding
dimensions are picked.

<diagonal_tol> Offset for picking diagonal peaks.

See also: read_spectrum, spec_noise

Further reading:

- Wuerz & Guentert. J. Biomol. NMR 67, 63-76 (2017)
