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Analysis of the 
high quality domains shows that the maximum
distance 
between axial coordinates that can be bridged by a
loop of 
residues is 
Å.
Maps having any loop with distances larger than 
Å
are removed. 
Å is added to allow for differences in the packing of
database and query secondary structures, since similar structures with
little sequence similarity can have shifts of up to Å [Holm \& C., 1995].
Care is taken to allow a range of possible positions for the match of
query and database structures. This allows for errors in secondary
structure prediction, which may fail to predict the precise start or end of
correctly identified elements, and allows for the observed differences between
the lengths of secondary structure elements within proteins having similar
topologies despite no significant sequence similarity.
For a position 
on a
database secondary structure, and a minimum and maximum length
for a query secondary structure, 
and 
, the range
of allowable positions of the query residue on the database structure
(of length 
) is given by:
min 
max 
where 
is a leniency parameter, allowing for differences in
the length of query and database secondary structures. 
allows for differences typical of those found in proteins having
similar 3D structures despite no sequence similarity.