TM-score FAQ
Q: There are mismatches when I compare my model with PDB files.
A: TM-score only compare the common regions where both model and PDB structure have
avaliable coordinates. The common regions are decided by the residue sequence number (Column 23-26
in PDB format).
It is user's responsibility to keep the equivalence of compared residues in both pdb files.
Q: Can I specify the chain identifier?
A: No. TM-score automatically reads all C-alpha coordinates from input files. Users usually should
re-edit the orginally PDB file and keep only the compared residues in the PDB files before runing TM-score.
Q: When I run TMscore in my local machine, I get a warning message: "bash: ./TMscore: cannot execute binary file".
A: You need to download another compiled version.
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