SWISS-MODEL (i.e. ProModII) also computes a confidence factor for each atom in the model structures. This "Model B-factor" is included in the PDB file returned to the user and occupies the normal B-FACTOR field. Programs such as the Swiss-PdbViewer allow the colouring of the structure according to this variable (i.e. colour temperature). The Model B-factors are determined as follows:

1. The number of template structures used for model building.
2. The deviation of the model from the template structures.
3. The Distance trap value used for framework building.

85.0 * (1/ # selected template str.) * (Distance trap / 2.5)

and

99.9 for all atoms added during loop and side-chain building.

Sequence information is also not respected by the factor computation.

This way of computing the Model B-factors will indicated if:

• A model was built based on one or more template structure. A model build upon only one template structure has a lower confidence (higher Model B-factor) than one built using several template structures.
• Should one or more of the template structures deviate to much from the others (more that distance trap), then the factor <<# selected template str.>> will decrease and the B-factor increase. This indicates a higher variablitiy in the considered region.
• If the distrance trap is higher than 2.5 Ang. then the Model B-factors will be increased, since a higher variability is allowed. The opposite is true if the selected distance trap is lower than 2.5 Ang. (Default in ProModII is 2.5 Ang).
• All fully rebuilt atoms are very hot.

• Sequence information is not used by ProModII to comput Model B-factors. This means that a model built with only one template structure, but being 99% identical with the template will have far higher B-factors than it should. However, this is felt to be unimportant, since in this case (only one or few changes) it is obvious that quasi identical sequences will have very very similar structures.