(See the Files form for instructions on how to specify input files. See the Edit form for instructions on how to save data as either a PDB, DCD, or CRD file. The Edit form can also be used to append PDB and DCD files to a loaded molecule.)
If only a coordinate file (i.e. just a PDB, with no PSF) is given, two passes are made through the file. The first pass determines how many atoms exist and the second reads them in. VMD then uses internal defaults to fill in the missing values. It then does a distance search to determine the bond connectivity, which will make some strange bonds if atoms are too close. If both a PSF and a PDB file are given, no approximations or guesses are made. For those interested in the details, when VMD is forced to guess the connectivity, it considers a bond to be formed whenever two atoms are within of each other, where and are the respective radii of candidate atoms.
After the molecule is read, VMD checks to see if any new names are needed for the various coloring categories. If so, they are created and assigned a new color. (When the end of the color list is reached, the color starts again at the beginning.) Next, the bond connectivity is established and the molecule is analyzed to identify the various components, i.e., determine which residues are protein, nucleic acids, and waters, which atoms are backbone atoms, etc. A search is then made to connect these different types into larger fragments of the same type. As these searches take place, the information is printed to the screen. An example output for BPTI is:
Info 1) Analyzing structure ... Info 1) Atoms: 898 Bonds: 909 Info 1) Backbone bonds: Protein: 231 DNA: 0 Info 1) Residues: 58 Info 1) Waters: 0 Info 1) Segments: 1 Info 1) Fragments: 1 Protein: 1 Nucleic: 0
There are actually several types of fragments. Protein and nucleic fragments are homogeneous; either all proteins or all nucleic acids. However, it is quite possible for a protein to be connected to a nucleic acid or some other non-protein. When this occurs, a warning message is printed, as in:
Warning 1) Unusual bond between residues 1 and 2
These warnings are known to occur with terminal amino acids, zinc fingers, myristolated residues, and poorly defined structures.