Run Pairwise Alignment

The server gives you access to the developmental version of jCE and jFATCAT. You can launch a pairwise alignment of the latest development code from below.

Chain based alignments

Specify what PDB chains to be aligned from here:
PDB1: Chain1:
PDB2: Chain2:

RCSB PDB Protein Comparison Tool

Stable release versions of this code base are also available from the RCSB PDB comparison tool at:


Pre-calculated Alignments

If the jFatCat algorithm is selected in the above form, the Java Web Start application communicates with the RCSB server hosting the all vs. all alignments and if available will download the pre-calculated alignment and visualize it. If it is not available, it will run the alignment locally and submit the result to the server.

Local PDB installations

If you have a copy of PDB installed locally, the application can be configured to use these files. The code supports either hierarchical PDB file organizations (as on the RCSB PDB ftp server) or all PDB files being located in one directory.

If you don't configure a PDB location, the files will be automatically downloaded and stored in the default Java Web Start application folder.

How to work with chain IDs and ranges
Chain IDs are case sensitive. If a lower case chain ID is provides, which is not found in the PDB file, the code attempts to convert the chain ID to upper case.

Ranges are defined by the following syntax: Example: A:123-333,B:10-20