I use PFAAT for this task and am very pleased with the results. http://pfaat.sourceforge.net/. PFAAT is a multiple sequence alignment (MSA) viewer that is integrated with Jmol to view structures. This gives you the ability to edit the alignment and quickly re-map the conservation scores.
1) Run PFAAT and open up a MSA with File-> Open.
2) Right click the sequence you have a PDB file for and select "Associate PDB Numbering With Structure" Select the chain you are interested in.
3) Calculate the conservation scores with Analysis -> Conservation Scores -> Information Score. There are a couple of options here, Shannon Entropy with the Blossum62 similarity matrix works well.
4) View the mapped scores in jmol with Analysis -> Map conservation scores to structure.
To change from wireframe representation to spacefill enter the following on the Jmol command prompt,
select all; wireframe off; spacefill; If the pdb has waters or non-protein atoms obscuring your view, remove them with
select hetero; spacefill off; Get rid of an extra chains with
select:X; spacefill off; where X is the chain letter to remove. For more information, refer to the Jmol documentation.
5) To edit the MSA, right click a sequence name and select "Delete sequence" from the menu then repeat steps 3 & 4.
6)If you would like to increase sequence conservation, View -> Sort Sequence By -> Percent Identity of Sequence. Select the sequence with the associated pdb, then delete sequences from the bottom of the list.
If you have any questions, leave a comment and I'll get back to you tomorrow.
Awesome! Thanks a lot.. I've been using Pymol mostly cause I love the interface and images it generates. I hope I find out something similar in pymol too.