You have the choice of computing the structural alignment using 3 approaches:

- based on the pairwise, global sequence alignment between the selected chains using the well-known least-squares fit (LSQ)

- based on MAMMOTH, a method not requiring any sequence similarity between the two structures, finding the best geometrical fit

- by giving the transformation matrix

DirectAccessURL

Structural alignment based on the pairwise sequence alignment:

http://i.moltalk.org/strx2strx/6/PDB/1QMZ/65/PDB/1FIN/65/?/seqbased

Structural alignment based on a strictly geometrical fit (MAMMOTH):

http://i.moltalk.org/strx2strx/6/PDB/1QMZ/65/PDB/1FIN/65/?/coordsbased

parameters:

toolchain
"strx2strx"
position
"6"
strx source 1
"PDB" or "model"
strx id 1
first structure, 4-letter pdb code or unique identifier of uploaded model
chaincode 1
first chain, ASCII value of chain identifier (A=65, B=66, ' '=32, ...)
strx source 2
"PDB" or "model"
strx id 2
first structure, 4-letter pdb code or unique identifier of uploaded model
chaincode 2
second chain, ASCII value of chain identifier (A=65, B=66, ' '=32, ...)
transformation matrix
only for action "trafobased"
alaction
either "seqbased" for the sequence alignment based structural alignment or "coordsbased" for the strictly coordinates based structural alignment (MAMMOTH) or "trafobased" for applying the explicitly passed transformation matrix