usage: cara2tab [-h] --in cara.peaks [--spinID cara.spins] [--ft test.ft2]
[--order ORDER] [--cal [C [C ...]]] [-e EXP [N ...]]
[-c VAR FMT DEFAULT] [--out cara.tab]
Convert a CARA anchor or strip peak list to NMRPipe .tab file
Assignment
----------
CARA uses the Xeasy format for its peak lists. This format does not
contain assignment data directly. Instead, it includes a spin ID
number for each chemical shift in the peak list, where each spin ID
number corresponds to a spin within CARA.
Assignment data must be added to STRIP peak lists using a spin ID file.
Spin ID files are generated using the CARA Lua script included in the
nmrpeaklists library. Use the --spinID option to provide this spin ID
file.
If no spin ID file is provided, it will be assumed that the peak list is
an ANCHOR peak list. CARA anchor peak lists include the assignment data
for each data line as a comment immediately following it. In this case,
the assignments can be extracted directly from the peak list. No spin ID
file is required.
Correspondence to an NMRPipe spectrum
-------------------------------------
If you plan to use the NMRPipe .tab file with nlinLS to fit data, then
the peak list will correspond to a particular NMRPipe spectrum. The
script needs access to the header of that spectrum to correctly
calculate the location of each peak in units of points. Use the --ft
option to provide the spectrum. It can be either a monolithic file or
the first plane from a series.
Beware, the order of the columns in the peak list may not match the
order of dimensions in the spectrum. Use the option --order to specify
which column of the peak list (from left to right) corresponds to which
dimension in the NMRPipe spectrum (XYZA).
Use the --cal option to enter the calibration for each dimension in PPM.
The order here should match the order of dimensions in the NMRPipe
spectrum. These values should be the same as the calibration values in
CARA.
nlinLS Columns
--------------
If you plan to use the .tab file for fitting data with nlinLS, then you
will need to add the appropriate fitting columns. Columns can be added
in pre-set groups based on common experiments, or they can be added
individually.
Use the '-e' option to add all the fitting parameters needed for one of
the experiment types listed. Use the '-c' option to specify individual
parameter columns. Columns specified with the '-c' option will
overwrite corresponding columns set with '-e'.
You must provide three values when specifying a column with '-c'. The
first two are the values that appear in the VARS and FORMAT lines of
the NMRPipe .tab file, respectively. The final value will be the default
value used for each peak in the column.
In some cases, several columns are related to one another. These fall
into two categories, either there is one column for each dimension
(e.g. XW, YW, ZW) or there are multiple columns for a single dimension
(e.g. Z_A0, Z_A1 ...). In these cases, use '%s' or '%d' in the VARS
string to indicate that the string should be expanded with dimension
labels (X, Y, Z ...) or with list indices (0, 1, 2 ...), respectively.
The default values for these columns must be specified as a Python list.
List multiplication and addition syntax is supported here
(e.g. [1]+[0.5]*64), but the list MUST NOT include any spaces.
Supported Experiments
---------------------
The following pre-made experiment types are available. Use the given
experiment name with the '-e' option to add the corresponding nlinLS
fitting columns to the .tab file. Some experiments take a second
argument to the '-o' option. See the notes for an explanation.
The columns HEIGHT and XW, YW, etc. are added for all experiments.
Experiment Columns Notes
---------- ------- -----
Volume VOLUME
R1 Z_A
R2 Z_A
Het-NOE Z_A0, Z_A1
CEST N Z_A0 - Z_A(N) N = profile points+1 (for reference)
RD N Z_A0 - Z_A(N) N = profile points+1 (for reference)
The default value for each column added is provided in the table below.
These values can be overridden with the '-c' option.
Column Default
------ -------
HEIGHT 5e7
XW, YW, ZW, AW 2
VOLUME 0
Z_A (R1) -1
Z_A (R2) -10
Z_A0 (Het-NOE, CEST, RD) 1.0
Z_A1 (Het-NOE) 0.75
Z_A1, Z_A2, ... (CEST, RD) 0.7
Examples
--------
cara2tab --in strip.peaks --spinID cara.spins --ft NOESY.ft3
--order ZXY --cal 0.01 -0.05 0.11 -e Volume
cara2tab --in anchor.peaks --ft test.ft2 -e R1
cara2tab --in anchor.peaks --ft test.ft2 -e R1 -c HEIGHT %12.5e 1e8
cara2tab --in anchor.peaks --ft test.ft2 -e R2 -c %sW %6.3f [8,5]
cara2tab --in anchor.peaks --ft test.ft2 -e CEST 33
-c Z_A%d %8.5f [1]+[0.6]*32
optional arguments:
-h, --help show this help message and exit
--spinID cara.spins CARA spin ID file
--ft test.ft2 NMRPipe spectrum
--order ORDER correspondence between CARA peak list columns (left to
right) and spectrum dimensions (XYZA), default XYZA
--cal [C [C ...]] calibration for each dimension of the .ft file (in PPM)
-e EXP [N ...] Pre-made experiments: Volume R1 R2 Het-NOE RD CEST
-c VAR FMT DEFAULT Create custom column
--out cara.tab NMRPipe .tab file (default cara.tab)
required arguments:
--in cara.peaks CARA peak list