VMD User's Guide

–movetoposition: move all the atoms to a given location.–lmovetoposition list: move each atom to a point given by the appropriate list element.– writeXXX filename: write the selected atoms to a file of type XXX; e.g., pdb, dcd.New in VMD 1.8: writepdb requires a filename; omitting the filename no longerreturns the PDB data as a string. To get the PDB data as a string, first write to a file,then enter the following commands: set fd [open filename r]; set s [read $fd];close $fd. The text will be contained in the variable s.–update: Update the atom selection based on the frame for the selection (the frame canbe specified using the frame option as described above).See section 11.2 for more on using atom selections for fun and profit, as well as issues relatingto speed of analysis scripts.8.3.3 axesThe axes (orthogonal vectors pointing along the x, y, andz directions) can be placed in any of 5locations on the screen, or turned off.• locations: Return a list of possible locations.• location: Get the current location.• location < off | origin | lowerleft | lowerright | upperleft | upperright >: Positionaxes.Also, though this may seem like a likely command for changing the color of the axes, thisfunction can only be performed from the Colors form or by the color command (see below).Future implementations of VMD may change this.8.3.4 colorChange the color assigned to molecules, or edit the color scale. All color values are in the range0 . . . 1. Please see the section on coloring [§ 5.2] for a full description of the various options.• category name color: Set color of object specified by category and name to color.• scale method < scale name >: Set type of scale to use for coloring objects by values. Theyare:– RGB – Red to green to blue.– BGR – Blue to green to red.– RWB – Red to white to blue.– BWR – Blue to white to red.– RWG – Red to white to green.– GWR – Green to white to red.– GWB – Green to white to blue.94