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Click on the [?] for help on each option.
Type of alignment: [?]
Sequential alignment           Score to be maximized: TM-Score Structal Triangular score* [?]           Penalization for gaps: Default Custom: [?]
Non-sequential alignment (it is reasonable to uncheck the "Write sequence" option)           In this case, the non-bijective triangular* score will be maximized. [?]
*Distance cutoff for triangular scores:Å
Options:
Write sequence alignment (meaningful for one-atom-per-residue selections only) [?]
Use squential internal distance initial point [?]
Structures (PDB format): (1 will be aligned to 2)
Structure 1:
Selection:	[?]
Structure 2:
Selection:	[?]
Note:
The output contains all atoms of the original pdb file rotated and translated according to the best alignment obtained for the chain or molecule considedarkblue.