TM-align Update history
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Added an option "-seq" in the C++ version to calculate TM-score of two structure based on
sequence alignment. This is useful mostly for calculating TM-score between predicted
model and the native structure (see
https://zhanggroup.org/TM-score/help/ for detail.
TM-align was extended to
US-align which enables monomeric and complex structural
alignments between different macromolecules (proteins, RNAs and DNAs).
added output scripts for pymol, C++ version was included in the package.
Fixed multiple bugs associated with mmCIF formats
Enabled TM-align to support both PDB and mmCIF formats, and fixed a bug on file output
Added one iteration in initial4 to avoid asymmetric alignment
fixed a bug on conformation output
optimize I/O and increased speed by ~100%
Added 'TM.sup_all_atm_lig' to display ligand structures
Fix a bug in array overflow
Update TM-align so that it can read all alternate location
indicators and residue insertions
Add an option '-I align.txt' to allow user to STICK TO the
inital alignment. This is different from '-i align.txt' where
initial alignment can be optimized.
2012/05/07: Improved RMSD calculation subroutine which speeds up TM-algin
program by 10%.
2012/04/19: Add additional output file 'TM.sup_atm' for showing all-atom
superposition while 'TM.sup' and 'TM.sup_all' are only for C-alpha traces
2012/04/17: Add an option '-m matrix.txt' to output the rotation matrix
in separate file, drop-off secondary-structure smooth
procedure, and add one iteration in initial5. This change
increases the alignment accuracy (TM-score) by 2%.
2012/04/16: Add an option to allow user to specify seed alignments, e.g.
'-i align.txt'. This is used together with other inherent
TM-align seeds. An example of the fasta file can be seen at
2012/01/24: Fix a bug for secondary structure definition
2011/10/11: Distance cutoff for gap is increased from 3.85A to 4.25A.
Added 'TMalign -v' to allow user to check version number.
2011/10/11: A new scale (d0) was introduced for alignment search. This
is to mainly improve alignment selection for small proteins
(e.g. L<50 residues) but also increase alignment coverage
of larger proteins. Second, TM-align output format is changed
and two TM-scores normalized by both chains are reported.
- 2011/09/03: A new option "-d" is added to allow users to change
TM-score normalization scale. A version number is attached
to the program from now on
- 2011/01/30: An open source license is attached to the program
- 2011/01/24: Fixed a bug on output file name created on 2011/01/03.
- 2011/01/03: The length of pdb file names were extended to 500.
- 2010/08/02: A new RMSD matrix was used to remove obsolete statements.
Staled subroutines were deleted.
- 2009/08/20: A bug for asymmetry alignment result was fixed.
- 2009/03/14: A new initial alignment was added and previous initial
alignments are further enhanced. This change increased
accuracy by 4% but increases CPU cost by 40%.
- 2007/10/16: A bug for irregular bond-length models was fixed.
- 2007/09/19: added a new feature alignment to deal with the problem
of aligning fractional structures (e.g. protein
- 2007/05/23: added additional output file 'TM.sup_all' for showing
all atoms while 'TM.sup' is only for aligned atoms
- 2007/04/18: added options with TM-score normalized by average
length, shorter length, or longer length of two
- 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
- 2006/06/20: select 'A' if there is altLoc when reading PDB file.
- 2005/10/19: the program was reformed so that the alignment
results are not dependent on the specific compilers.
- 2005/06/01: A bug of two-point superposition was fixed.