(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 or PSF 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 for some strange bonds if atoms are too close. If both a PSF a PDB file are given, no approximations or guesses are made.
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, ie, determine which residues are protein, nucleic acids, and waters, which atoms are backbone atoms, and so on. A search is then made to connect these different types into larger fragments of the same time. 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 strutures.