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Article ID: 1535 - Last Modified: January 3, 2012

My Phase Find Matches job stops with the following error:

PhpLigandFactory::generateLigands: The number of base features in mol_mumber does not match the number of sites stored in the database for this molecule.

How can I avoid this failure?

The error message also indicates that there are either differences between the hypothesis and database feature definition files, or that changes have been made to the hydrophobic feature perception libraries since the database was built. In Suite 2011, a change was made to a particular ring structure to classify it as aromatic rather than nonaromatic, so this is another possible source of the error message.

Given the change in the classification of this ring structure, you should regenerate the sites in the database, using the 2011 release. However, if you want to keep the site definitions in your database, you can run the search by generating sites during the search. You can do this in the Find Matches to Hypothesis panel by selecting "Generate sites during search" in the Matching tab, after selecting "Find new matches".

Another possibility is to exclude the problematic compound from the search by commenting out the LIGAND_NAME record for mol_number in the master subset file (dbname_master_phase.inp) by typing a '#' in the first column.

If you are concerned that the feature mapping is incorrect, you can send the problematic structure to for examination.

Note that this problem does not occur with the new phase_find_matches program, which uses the new database format generated with phase_database.

Keywords: Phase, database, search

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