In most visualization programs specific colors are associated with specific elements. However in a LAMMPS data file that atoms are only identified by their type and thus the embedded data file reader in the topotools package imports those as atom names (unless a very special extended data file syntax is used). The TopoTools plugin has some utilities to help with this process and other VMD script commands can be used to help as well. However, it is important to note that this process can it automated form only recover information that is present in the data. Since the generation of a data file usually means that unneeded information is lost, further reconstruction requires additional knowledge about the system in the data file. The first example discusses the reconstruction of a .psf/.pdb file for a bulk HDPE data file, data.hdpe-x5 using the script reconstructhdpe.tcl.

The process starts with reading in the data file (note: the atom style has to be known):

With this information loaded, we would get a visualization like in the left side of the image. Now we can try to guess the element names from the atomic masses and use those to set other properties like atom name or radius. Of course, this step only works, if the masses are actually given in the data file:

Finally we let VMD reanalyze the molecular information and write out the information in the desired formats:

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Combine multiple data files with overlap detection and removal

of course this strategy can be easily extended to merge more than two sets of molecules.