People interested in using 3D structures might like Aquaria, a new, free and open-source web resource for biologists that simplifies the process of gaining insight from protein structures (O'Donoghue et al., Nature Methods, 2015). For all SwissProt protein sequences, Aquaria provides a concise visual summary of all related 3D structures, and the facility to map features onto related structures (e.g., SNPs, PTMs, domains, etc.), including user-defined features (see API docs).
The Aquaria team (including Sean O'Donoghue, Kenny Sabir, Christian Stolte, Andrea Schafferhans)
There are some PDB files that I cannot find in Aquaria - why is that?
There may be several reasons: (1) If a PDB entry is relatively new, it may be missing from the sequence-to-structure alignment database that underlies Aquaria (called PSSH2). If the PDB entry is older than three months, please post the BioStars forum. (2) Currently, Aquaria does not include PDB structures that exceed the size of the traditional PDB file format limits (>62 chains or >99,999 atoms).
Why can't I see the amino acid sequence under the 3D structure?
Can I see a multiple sequence alignment view of the information in the Matching Structures section?
Aquaria is not designed to enable detailed viewing and editing of MSAs. However, using the Aquaria API you can fetch information on the alignments shown in the 'Matching Structures' section. You could then reformat and display that information in a program designed to show and edit MSA details, e.g., Jalview.