CYANA Command: atoms set

Parameters

selection=atom selection

(default: none)

mass=string

(default: none)

radius=string

(default: none)

shift=string

(default: none)

calibration=string

(default: none)

tolerance=string

(default: none)

residue=string

(default: none)

random=real

(default: 1.0)

protlev=real

(default: none)

rho=real

(default: none)

tauc=real

(default: none)

occupancy=real

(default: none)

undefined

all

Description

Sets properties of the selected atoms. By default, the selection made in the most recent atoms select command is used, or all atoms if no selection has been made so far. Properties that can be set:

mass

Atomic mass for torsion angle dynamics. If the mass value is a positive real number, the mass of all selected atoms is set to mass. In this case all inertia tensors are calculated from the masses and positions of their constituting atoms. If the special value mass=cluster is set, then the inertia tensors of all rigid units are set as if the rigid units were spheres of radius 5 Å with mass m, where m is the sum of the atomic masses within the rigid unit. Inertia tensors are initialized in this way when the program starts. Atomic masses are initialized to unity.

radius

Repulsive core radius in Å. The standard repulsive core radii are set in the ATOMTYPES section of the residue library.

shift

Chemical shift (in ppm).

calibration

Constant to derive distance bounds from peak volumes.

tolerance

Chemical shift uncertainty (in ppm).

residue

External residue number. The external residue number is changed for all residues for which at least one atom is selected.

protlev

Used to set the protlev parameter of selected atoms for eNOE calculations. The protlev parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * enoe spindiff

rho

Used to set the rho parameter of selected atoms for eNOE calculations.

tauc

Used to set the tauc parameter of selected atoms for eNOE calculations.

occupancy

Used to set the occupancy parameter of selected atoms for writing multi-state structure files.

undefined

The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option all, the coordinates of the selected atoms are set as “undefined” also in all selected structures.

Optionally, the command can be applied only to a random fraction of all selected atoms.