Pymol sessions
   
If you are new to PyMOL, consider skimming through the QuickStart page on PyMOL's wiki. In particular, you might want to read about PyMOL sessions.
   
Conservation module of Cube server produces Pymol session with the conservation score mapped on the selected chain of the uploaded structure.
   
The remaining chains and heteroatoms present in the PDB file are indicated in schematic way: peptide chains as dark teal-colored ribbons, small molecules as dark-teal sticks, and "structural" waters (the ones which carry chain label identical to the one selected in the analysis) as light teal-colored speheres. Metal ions, if present, are indicated as magenta spheres.
   
Read more about structure viewing and using PyMol.
   
Specialization module of Cube server produces Pymol session with both the specialization and the conservation score mapped on the selected chain of the uploaded structure. The other elements present in the PDB file are indicated similarly as in the conservation case above.
   
The difference now is that you can turn off the conservation visualization to reveal - in this order - several other things one can look for in contrasting the sequences:
  1. 'Discriminant' positions - positions that are well conserved within each group under consideration but different across different groups (labeled as 'specificity' in the Pymol session).
  2. Conservation within the reference group (that would be the group to which your reference sequence belongs)
  3. 'Determinants' for your group - positions that are relativealy well conserved in the reference group, and different then in the remaining groups (note that now we are not saying anything about the conservation status in other groups. The position may be conserved or variable in the other groups, as long as the overlap with the aminio acid types in the reference group is small).
The other elements present in the PDB file are indicated similarly as in the conservation case above.