T-Coffee: Tree-Based Consistency Objective Function for Alignment Evaluation - Multiple Sequence Alignment Methods - page 122

4. When using external database via their respective Web servers,
the results can vary with the upgrade of these databases. More-
over, when these servers are unavailable, the T-Coffee modes
requiring these databases will not be able to deliver an align-
ment. A solution would be to install locally the external servers
you require ( see corresponding external servers).
5. When using structure files as templates, PDB files are recognized
only when following the PDB standard format. If the PDB struc-
ture files are modified, they might no longer be recognized by
T-Coffee. If you want to do so, you should use T-Coffee refor-
matting options to modify the PDB file (cf. T-Coffee Tutorial).
It is particularly adapted to extract chains, parts, or blocks using
the reformatting option -other_pg extract_from_pdb specify-
ing the chain and the boundaries of the sequence of interest
( see T-Coffee Tutorial at http://www.tcoffee.org/Projects/
tcoffee/ ).
6. When using structural aligner, having available structure files
does not mean that the structural aligner will successfully
structurally align your sequences with their corresponding
templates; in such case, an error message will be printed out
and the alignment will be performed using the T-Coffee default
sequence aligner ( see step 3 in Subheading 3.1 ).

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