Quick guide

Loading data

• Load PDB file — opens a local .pdb or .cif.
• Fetch RCSB — type a 4-character PDB ID (e.g. 1IED) and press Enter.
• Load MSA — accepts FASTA (.fasta, .fa) or Clustal (.aln, .clustal); format auto-detected.
• For multi-chain PDBs, a chain selector appears (defaults to the longest chain).

Sequence matching

• The MSA row most similar to the PDB chain is auto-matched, highlighted yellow with a MATCH badge, and locked on.
• Toggle other sequences with the checkboxes — conservation recomputes instantly.
• All on / All off for bulk toggling (the matched row stays on).

Conservation

• % pairwise identity (default): mean identity over all pairs of active sequences at each column. Gap-rich columns score lower.
• Shannon entropy: information-theoretic measure; gaps excluded.
• Color ramp  cyan (variable) → white → maroon (conserved).

3D view

• Mix any of Cartoon · Stick · Sphere · Line · Surface by toggling the buttons.
• α slider controls surface transparency.
• Default on MSA load: Stick + Surface at α = 0.80.
• Mouse: left-drag rotate · scroll zoom · right-drag pan.

Linked selection

• Click a residue in the 3D view → highlights its MSA column.
• Click a residue cell in the MSA → labels the matching residue on the structure.
• Residues outside the alignment are labeled and the column highlight clears.
• Esc clears all highlights and labels.

Export to PyMOL

• Export PyMOL downloads a self-contained .pml script.
• Conservation (current metric, scaled 0–100) is written to the B-factor column for mapped residues; unmapped residues get B = −1.
• Open in PyMOL with File → Run Script… or pymol session.pml — it loads the structure and applies the same cyan→white→maroon ramp.
• To convert to a .pse: run pymol -cq session.pml -d "save session.pse; quit", or open in PyMOL and use File → Save Session As….

No MSA loaded