I got the following error when trying to build a homology model in Prime:

WARNING Errors occurred while incorporating Build Structure job

In the log file, I see this error message:

ERROR: mismatch in length of COMPOSITE_ARRAY and query sequence for template template1_A

This error can sometimes occur when using web-based homolog searches. When running Comparative Modeling (Structure Prediction) from databases on the web, the BLAST search only returns the aligned portion of the template sequence, not the full sequence. The web-based installation includes the sequence database from the PDB, but it is a static copy. If the BLAST search returns a match to a sequence that is not in this static copy of the database, the initial alignment displayed in the Find Homologs step will not be correctly aligned to the query sequence, and building the structure using this initial alignment may fail.

There are two possible workarounds:

1. Run an Align job in the Edit Alignment step. This job should correct the alignment in the sequence viewer, and allow the template to be used for building. You can also manually edit the alignment.


2. Download and import the template PDB structure manually, by choosing Project > Get PDB in the main window and downloading the desired structure, then choosing Import in the Find Homologs step to import the full sequence.

Another possible workaround (so that you don't have to go through the workflow again) is to build your structure from the command-line using the job files that the failed job produced. You should first delete the COMPOSITE_ARRAY line from the jobname.inp file and then run the job as follows:

$SCHRODINGER/bldstruct jobname

The COMPOSITE_ARRAY is important when using multiple templates, but can be removed for a single-template run.

Keywords: Prime, build structure, web-based search, NCBI, fail

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