VMD User's Guide

last frame. If the frame is a specific integer, the selection will always use coordinatesfrom that frame, even if the current animation frame changes. Note that if a nonexistentframe is specified, the atomic coordinates will reference the last frame.–frameframe: Set the frame for the selection. frame should be either now, last, oraninteger.– delete: Delete this object (removes the function).–global: Moves the object into the global namespace. Atom selections created within aTcl proc that are not made global are deleted when the proc exits.– uplevel level: Moves the object to a new level in the namespace stack. Works the sameas the Tcl function uplevel.–getattribute list: Given an attribute or a list of attributes, returns the attribute values.If only a single attribute is given, a list of corresponding attributes values will be returned.If a list of attributes is given, then a list of sublists will be returned; each sublistwill contain the values for the corresponding attributes. See Tables 5.5, 5.6, and 5.8 forthe recognized attribute keywords.–setattribute list values lists: Set the attributes in the attribute list with the values gvenin the values lists. If there is only one attribute, then values lists can be either a singlevalue or a list of values, one for each selected atom. If there is more than one attribute,then values lists must be a list of sublists; the number of sublists must equal the numberof selected atoms, and the number of items in each sublist must equal the number ofattributes.Example:set sel [atomselect top all]set mass [$sel get mass]set xyz [$sel get {x y z}]$sel set beta 0 # all values are set to zero$sel set beta $mass # copy mass to beta# set occupancy to x, mass to y, beta to z$sel set {occupancy mass beta} $xyzIt is an error to set integer or floating point keywords using non-numeric values. Iffloating point values are passed to integer keywords, they will be converted to integers,and vice versa.The set command immediately updates all representations of the selected molecule. Ifspeed is an issue, delete all representations of the molecule before setting the values.– getbonds: returns a list of bondlists; each bondlist contains the id’s of the atoms bondedto the corresponding atom in the selection.– setbonds: Set the bonds for the atoms in the selection; the second argument should bea list of bondlists, one bondlist for each selected atom.–move4x4 matrix: Applies the given transformation matrix to the coordinates of eachatom in the selection.–movebyoffset: move all the atoms by a given offset.–lmovebyoffset list: move each atom by an offset given in the list.93