Subsections


pcs.read

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Synopsis

Read the PCS data from file.

Defaults

pcs.read(align_id=None, file=None, dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None)

Keyword arguments

align_id: The alignment ID string.

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

dir: The directory where the file is located.

spin_id_col: The spin ID string column (an alternative to the mol, res, and spin name and number columns).

mol_name_col: The molecule name column (alternative to the spin_id_col).

res_num_col: The residue number column (alternative to the spin_id_col).

res_name_col: The residue name column (alternative to the spin_id_col).

spin_num_col: The spin number column (alternative to the spin_id_col).

spin_name_col: The spin name column (alternative to the spin_id_col).

data_col: The PCS data column.

error_col: The experimental error column.

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

spin_id: The spin ID string to restrict the loading of data to certain spin subsets.

Description

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

The spin system can be identified in the file using two different formats. The first is the spin ID string column which can include the molecule name, the residue name and number, and the spin name and number. Alternatively the molecule name, residue number and name, and spin number and name columns can be supplied allowing this information to be in separate columns. Note that the numbering of columns starts at one. The spin ID can be used to restrict the reading to certain spin types, for example only 15N spins when only residue information is in the file.

Prompt examples

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

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

To read the 15N and 1H PCSs from the file `Eu.txt', where the 15N values are in the 4 th column and the 1H in the 9 th, type both the following:

[numbers=none]
relax> pcs.read('Tb', 'Tb.txt', spin_id='@N', res_num_col=1, data_col=4)

[numbers=none]
relax> pcs.read('Tb', 'Tb.txt', spin_id='@H', res_num_col=1, data_col=9)


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