CYANA Command: atoms set: Difference between revisions
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:; '''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. | :; '''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. | :;'''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). | |||
shift Chemical shift (in ppm). | :;calibration :Constant to derive distance bounds from peak volumes. | ||
calibration Constant to derive distance bounds from peak volumes. | |||
tolerance Chemical shift uncertainty (in ppm). | 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. | residue External residue number. The external residue number is changed for all residues for which at least one atom is selected. | ||
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 of the selected atoms coordinates are set as “undefined” also in all selected structures. | 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 of the selected atoms coordinates are set as “undefined” also in all selected structures. | ||
Optionally, the command can be applied only to a random fraction of all selected atoms. | Optionally, the command can be applied only to a random fraction of all selected atoms. | ||
Revision as of 13:46, 6 August 2009
Parameters
- selection=string
- (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)
- 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. 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 of the selected atoms coordinates are set as “undefined” also in all selected structures. Optionally, the command can be applied only to a random fraction of all selected atoms.