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Article ID: 997 - Last Modified: February 17, 2011

PrimeX stopped in the middle of refinement with the error message, "number of iso-/aniso-tropic atoms does not match input". What does this error mean and what can be done to solve the problem?

In the log file for the job that that failed, approximately 50 lines before this error message appears, should be the sentence, "There are atoms in the PDB file with no match in memory...". Below this sentence there is a list of one or more atoms that are not consistent with normal molecular stereochemistry. For example, one carbonyl carbon of the peptide backbone may have a hydrogen attached to it.

Use the Find facility in Maestro to examine these atoms. Correct the structure as necessary and try executing the job again. This issue is most frequently seen when starting a new refinement using a problematic structure from the PDB.

Also, check the top of the log file for any messages that begin "mmlewis warning". The software may have resolved these problems automatically, but it is still worth checking that the resolution steps were chemically correct.

Keywords: PrimeX, refinement, fail

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