	SEQMOL index

Linking sequence alignment and PDB coordinates Download

	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), ATOM 1 N LEU A 670 43.020 9.594 120.671 1.00 0.80 N ATOM 2 CA LEU A 670 42.263 10.842 120.659 1.00 0.80 C ATOM 3 C LEU A 670 43.111 12.086 120.381 1.00 0.80 C ATOM 4 O LEU A 670 43.194 12.565 119.250 1.00 0.80 O ATOM 5 CB LEU A 670 41.513 11.035 121.989 1.00 0.80 C ATOM 6 CG LEU A 670 39.983 11.137 122.012 1.00 0.80 C ATOM 7 CD1 LEU A 670 39.471 11.187 123.442 1.00 0.80 C ATOM 8 CD2 LEU A 670 39.509 12.363 121.248 1.00 0.80 C ATOM 9 N LYS A 671 43.773 12.571 121.425 1.00 6.11 N ATOM 10 CA LYS A 671 44.081 13.996 121.553 1.00 6.11 C ... END - "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: