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/* Internals of the algorithm */
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_wikis/BioJava:CookBook:PDB:alignGUI.md

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@@ -55,7 +55,7 @@ interact with Jmol see <BioJava:CookBook:PDB:Jmol>.
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Internals of the algorithm
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The \*Distance Matrix\* button shows the distance matrix that is used
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The **Distance Matrix** button shows the distance matrix that is used
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internally for the alignment and the path that has been choosen.
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![](DistanceMatrix.png "DistanceMatrix.png")

_wikis/BioJava:CookBook:PDB:alignGUI.mediawiki

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@@ -37,10 +37,9 @@ The '''Show in Jmol''' button allows to display this alternative alignment in Jm
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[[Image:AlignmentJmol.png]]
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== Internals of the algorithm ==
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The *Distance Matrix* button shows the distance matrix that is used internally for the alignment and the path that has been choosen.
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The '''Distance Matrix''' button shows the distance matrix that is used internally for the alignment and the path that has been choosen.
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[[Image:DistanceMatrix.png]]
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==Configure PDB installation (Optional)==
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If you have a PDB installation that contains all PDB files in a single directory you can configure the System property PDB_DIR to point to this directory. (e.g. at startup specify -DPDB_DIR=path/to/PDB/files )

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