Subsections


interatom.read_dist

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Synopsis

Read inter-spin distances from a file.

Defaults

interatom.read_dist(file=None, dir=None, unit=`meter', spin_id1_col=1, spin_id2_col=2, data_col=3, sep=None)

Keyword arguments

file: The name of the file containing the averaged distance data.

dir: The directory where the file is located.

unit: The unit of distance. The default is meter, but Åcan also be specified.

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 distance data column.

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

Description

This allows interatomic distances to be read from a file. This is useful in the case when the distances vary, avoiding having to tediously use the interatom.set_dist user function for each spin-pair separately. The format of the file should be columnar, with the two spin ID strings in two separate columns and the distances in any other. The default measurement unit is meter but this can be changed to Å.

For RDC and relaxation based analyses, as the magnetic dipole-dipole interaction is averaged in NMR over the interatomic distance to the inverse third power, the interatomic distances within a 3D structural file are of no use for defining the interaction. Therefore these rˆ-3 average distances must be explicitly defined.

Prompt examples

To load the distances in meters from the fifth column of the `distances' file, and where the spin IDs are in the first and second columns, type one of the following:

[numbers=none]
relax> interatom.read_dist('distances', 1, 2, 5)

[numbers=none]
relax> interatom.read_dist(file='distances', unit='meter', spin_id1_col=1, spin_id2_col=2, data_col=5)


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