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| This section is for stand-alone software packages that do not require a web browser. | | This section is for stand-alone software packages that do not require a web browser. |
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| ===Calculate Structure Alignment===
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| This is a java program (java web start) offered by the U.S. [[PDB]]. At [https://www.rcsb.org/pages/analyze_features#Sequence PDB Sequence & Structure Alignment]. You will then get a form where you can enter two [[PDB codes]] (or upload two PDB files), optionally with a sequence range for each. Alternatively, with the ''Database Search'' option, you can enter a single PDB code (or upload a PDB file), and find structure neighbors. On the right is a link "Align custom files (Launches a Java Web Start application)", which starts the ''Calculate Structure Alignment'' java software. This package offers java implementations of the CE and FATCAT (you can choose '''rigid''' or '''flexible''') algorithms (see above).
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| * Pairwise Comparison: displays the alignment in Jmol, and a sequence alignment (presumably structure-based).
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| * Database Search: I got no results after clicking "Align" for either jCE or jFATCAT - rigid. These options did not appear to be working. [[User:Eric Martz|Eric Martz]] 16:28, 4 October 2010 (IST)
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| * Help is minimal and results are not clearly labeled.
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| ===DeepView = Swiss-PDBViewer=== | | ===DeepView = Swiss-PDBViewer=== |
