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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | Notes on how this package can be tested.
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This package can be tested by executing
sh installation-test
in order to confirm its integrity.
Package contains 2 executable files - TMalign and TMscore.
Both are called in `installation-test` script.
To test manually, cd to some dir, where you have write permissions and do
cp -a /usr/share/doc/profbval/examples/* .
gunzip 1ni7.pdb.gz 5eep.pdb.gz
Then run
TMalign 1ni7.pdb 5eep.pdb
or
TMscore 1ni7.pdb 5eep.pdb
PDB structure files for this testsuite were picked randomly from RCSB PDB
database [1], based on sequence similarity (first I picked random protein
with 1 chain, then found similar structure with "Sequence Similarity Cutoff"
at level 95%). As a result, they have TM-score metric > 0.8.
By default, TM-align page [2] suggests for comparison pair of protein
structures with PDB ID "101m" and "1mba" - you can also run TMalign
with these two structures and compare your results with those stated
at Zhang Lab's site.
References:
[1]: RCSB PDB database
http://www.rcsb.org
[2]: TM-align page at Zhang Lab's site
http://zhanglab.ccmb.med.umich.edu/TM-align/
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