VMD User's Guide

Periodic TabThe Periodic tab controls the display of periodic images of a molecule. In order to display periodicimages, a molecule must have unit cell information set for a, b, c, alpha, beta, andgamma, whichare discussed in section 8.3.21. When the proper unit cell information is present, the periodicdisplay feature can show periodic images of the unit cell by transforming and rendering additionalcopies of the structure. The current implementation of this feature doesn’t provide for complexcrystallographic symmetry operations. Unit cells that can be replicated by translation along thethree unit cell axes are the only ones supported presently. The periodic images to be drawn areselected by enabling images in one or more of the six faces of the unit cell. The Self image selectsthe untranslated unit cell itself, so that one my render a representation consisting of only replicaimages. This feature allows the unit cell and its periodic images to be displayed using differentmaterials, for cases where it is desirable to draw more attention to the original unit cell or to oneore more of the replicas. The Number of Images counter controls how many replicas are made ineach of the six directions. Some file formats read by VMD may not include unit cell information, insuch cases you can use the scripting interface to set the unit cell information manually. PDB filescontaining CRYST1 records are an example of a file format that provides unit cell information.4.4.8 Labels FormFigure 4.8: The Labels formThis form is used to manipulate the labels which may be placed on atoms, and the geometrymonitors which may be placed between atoms. Labels are selected with a mouse, as discussed insection 4.1.2. Once selected, the Labels form can be used to turn different labels on or off or to deletethem entirely. Also, labels displaying geometrical data such as bond lengths may be graphicallydisplayed using this form.43