after running the scripts, it appears some errors:
...
KeyError: 'No such residue: 37:A'
Yes, that's the same error you reported before. Please read my previous
post.
The residue numbers in the model are really the same as residue numbers in the
template.
No - they're not. You are building a single-chain model, so Modeller
will not assign it a chain ID. And the residue numbers would only match
if your alignment contained no gaps.
After 'mod9v1 model-segment.py', it produce the 'tm-mrg.ini' and
'tm-mrg.scr'files, if the script is wrong, dose it produce results else?
You will also get one or more .pdb files if the script runs to completion.
ps: is there any diffference between the .ini files and .pdb files?
Of course - the .ini file is simply the target sequence threaded onto
the template structure. It is unoptimized.