It was stressed earlier that the quality of the homology model is controlled by the quality of the experimental structure used for modelling. This simply means that a good quality model requires a good quality experimental structure. The 2 most important determinant of the quality of an experimental structure is resolution and refinement. Generally, the higher the resolution and the lower the R-factor (which characterizes the refinement) the better the structure quality. Another essential quality indicator is the geometry of the model, which includes bond lengths, bond angles and the Ramachandran plot, discussed earlier. All these parameters are easily accessible on the PDB and PDBsum sites. PDBsum probably provides a good visualization option for structure quality. An example of the PDBsum page of the BchI entry 1g8p is shown below:
Apart from the name of the protein, title, etc., you can directly see the resolution of the structure and the R-factor. Clicking on the Ramachandran plot on the right will open a page with a larger version of the plot. And while there, we can choose to see the full report on the protein quality from the Procheck software by clicking the PROCHECK button:
Another important quality parameter to keep in mind is the temperature factor, B. The temperature factor shows mean-square displacement of coordinates of atoms in the molecule. These displacement can be a result of disorder in the crystal, but also due to flexibility of side chain and main chain atoms in the crystal. The temperature factor may provide useful assessment of local quality, since flexible parts of the structure tend to have high temperature factors, which also results in weak electron density (bad map quality), and thus poor local structure. Such regions can be easily visualized by coloring the molecule in the graphics program after the temperature factors. Red (hot) color usually marks regions with high flexibility. Such regions can also be inspected using the electron density server (EDS).
At this page we can start the Astex viewer, which will display the electron density of the molecule. We may center the view on one of the residues we are interested in by clicking on the sequence below the graphics window (not shown). There are several options in the program which may be used to modify the view of the model and the electron density. On the image below on the left, a region of a structure with good quality electron density is shown. On the right, one of the regions that has bad torsion angle values (outliers), and apparently weak electron density (and high temperature factors), is shown:
The weak density explains the poor geometry of this region. This illustrates how important the quality of the electron density is for model quality. It also shows that problems present in the template are imported to the homology model. Try yourself the EDS server and have a look at some structure, for example 1g8p.
The RCSB PDB also provides quality measures, although in this case they look like the QMEAN-style quality assessment by the Swiss Model server (although not QMEAN calculation as at Swiss Model). Clicking of the graph will take it us to the full quality report: