TM-score FAQ
Q: There are mismatches when I compare my model with PDB files.
A:
The dafault option of TM-score only compares the common regions where both model and PDB structure have
avaliable coordinates. The common regions are decided by the residue order number (Column 23-26
in PDB format).
If the residue order number is not ordered correctly, you can use
>TMcore -seq model native
to calculate TM-score, which decides the compared residues based on sequence alignment.
This option is only available for the C++ version of the TMscore program
(see https://zhanggroup.org/TM-score/help/ for detail).
Q: Can I specify the chain identifier for TM-score comparison?
A:
No. TM-score automatically reads all C-alpha coordinates from input files till a <TER> reached.
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:
The current program was compiled for 64 bit machine. If your computer is a 32bit machine,
you need to download another compiled version.
Q: Why should I recompile the TMscore.f in my machine?
A:
The executable TMscore file was generated in our machine which may have
a complete different architecture from your machine. Therefore, recomipling the
source code will greatly increase the speed and efficiency of the TMscore program
in your machine. The compiling commend for TMscore.f is:
>gfortran -static -O3 -ffast-math -lm -o TMscore TMscore.f
or
>g77 -static -O3 -lm -o TMscore TMscore.f
or
>g++ -static -O3 -ffast-math -lm -o TMscore TMscore.cpp
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