Prime User Manual - ISP

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Appendix D: Error Messages and Warnings
No Homologs Found
• You may change your search options and continue searching, or proceed to Fold Recognition.
Invalid File
• Check to ensure the homolog file exists in either of the following locations:
$SCHRODINGER/thirdparty/database/pdb/data/structures/divided/pdb/*
$SCHRODINGER_THIRDPARTY/database/pdb/data/structures/divided/pdb/*
and is in the right format (UNIX compressed, pdb*.ent.gz).
D.2.2 Warnings in Homologs Table
These messages appear in the Warning column of the Homologs table for sequences that are
likely to be unusable for model building:
Many missing residues
• Too many consecutive missing residues to guarantee model building will succeed.
!UNUSABLE: Alternate residue type
• The residue type was undetermined, causing the file to include the residue twice but with
different identity (e.g. ALA20 and VAL20). This is not supported by Prime.
!UNUSABLE: Bad SEQRES
• General problems with the SEQRES.
!UNUSABLE: CA only
• File contains only alpha C coordinates.
!UNUSABLE: Molecule molname should be labeled as HETATM
• A non-protein molecule has been listed as ATOM when it should be listed as HETATM.
ATOM records are reserved for proteins only.
!UNUSABLE: SEQRES/ATOM mismatch
• The sequence listed in the SEQRES records does not match the actual sequence in the
ATOM records.
!UNUSABLE: SEQRES is missing residues
• There are residues in the ATOM records that are not listed in the SEQRES records. PDB
files require that the ATOM records be a subset of the SEQRES records.
Prime 2.1 User Manual