SEQMOL index

Linking sequence alignment and PDB coordinates



To enable many useful features of the application, including PDB structure analysis, coloring of PDB by conservation and covariation, exploring sequence alignments + PDB in parallel (including establishing common residue numbering),

PDB file must be provided along with sequence alignment to the "Alignment 1" window by File-Open or drag-dropping,

 will become

The sequence of the PDB file's relevant chain should be among the aligned sequences.

PDB file should be in standard format (as output by PyMol, for example),

- "key sequence from PDB" should be selected
- number of the PDB sequence in the sequence alignment is the No. of the key sequence
- PDB chain is what was used in the sequence alignment (in this example, PDB chain A is sequence No. 42).

When settings are correct, double clicking a sequence position should return the number of corresponding amino acid in the PDB file: