Model CA Trace and Template PDB Files

Model CA Trace Coloured by SQUARE

This is your alignment converted into a model. The model is reconstructed from the alignment submitted to the server and the PDB coordinates of the template. SQUARE only reconstructs the CA coordinates. The results from SQUARE are also mapped onto each residue via the temperature feature in the PDB atom records. To view the predicted alignment reliablity scores, simply colour the PDB file by temperature. The highest scoring aligned residues will be red, intermediate scoring residues will run from orange, through yellow and green to light blue and finally the lowest scoring residues will be dark blue.

Entire Template PDB Chain Coloured by SQUARE

This PDB file is based on the entire template chain. This is the PDB file of the template chain with the results from SQUARE mapped onto each residue via the temperature feature in the PDB atom records. To view the predicted alignment reliablity scores, simply colour the PDB file by temperature. The highest scoring aligned residues will be red, intermediate scoring residues will run from orange, through yellow and green to light blue and finally the lowest scoring residues will be dark blue. Template residues that have no aligned residue will have a score of 0, but are still shown.

Part Structure Coloured by SQUARE

This PDB file is based on the entire template chain, but shows only those template residues that are aligned to a residue in the target. This is the PDB file of the template chain with the results from SQUARE mapped onto each residue via the temperature feature in the PDB atom records. To view the predicted alignment reliablity scores, simply colour the PDB file by temperature. The highest scoring aligned residues will be red, intermediate scoring residues will run from orange, through yellow and green to light blue and finally the lowest scoring residues will be dark blue.