Subsections


rdc.read

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Synopsis

Read the RDC data from file.

Defaults

rdc.read(align_id=None, file=None, dir=None, data_type=`D', spin_id1_col=1, spin_id2_col=2, data_col=None, error_col=None, sep=None, neg_g_corr=False, absolute=False)

Keyword arguments

align_id: The alignment ID string.

file: The name of the file containing the RDC data.

dir: The directory where the file is located.

data_type: Specify if the RDC data is in the D or 2D format, or the T = J + D format.

spin_id1_col: The spin ID string column for the first spin.

spin_id2_col: The spin ID string column for the second spin.

data_col: The RDC data column.

error_col: The experimental error column.

sep: The column separator (the default is white space).

neg_g_corr: A flag which is used to correct for the negative gyromagnetic ratio of 15N. If set to True, all RDC values will be inverted prior to being stored in the relax data store.

absolute: A flag which indicates that the loaded RDCs are are signless.

Description

This will read RDC data from a file and associate it with an alignment ID, either a new ID or a preexisting one with no RDC data.

The data type is used to specify how the RDC is defined. It can be set to a number of values:

`D' means that the splitting in the aligned sample was taken as J + D.
`2D' means that the splitting in the aligned sample was assumed to be J + 2D.
`T' means that the file contains T = J + D values.

Internally, relax uses the D notation. Therefore if set to `2D', the values will be doubled when read in. If the `T' data type is specified, then J couplings must be present for this data to be of any use.

If the negative gyromagnetic ratio correction flag is set, a sign inversion will be applied to all RDC values to be loaded. This is sometimes needed for 15N if the data is not compensated for the negative gyromagnetic ratio.

The absolute RDCs flag is used for RDCs in which the sign is unknown. All absolute RDCs loaded will be converted to positive values.

Prompt examples

The following commands will read the RDC data out of the file `Tb.txt' where the columns are separated by the symbol `,', and store the RDCs under the ID `Tb':

[numbers=none]
relax> rdc.read('Tb', 'Tb.txt', sep=',')

If the individual spin RDC errors are located in the file `rdc_err.txt' in column number 5, then to read these values into relax, assuming J + D was measured, type one of:

[numbers=none]
relax> rdc.read('phage', 'rdc_err.txt', data_type='D', error_col=5)

[numbers=none]
relax> rdc.read(align_id='phage', file='rdc_err.txt', data_type='D', error_col=5)


The relax user manual (PDF), created 2016-10-28.