Validation Server: Possible Format Problems

# Structures may be deposited to the PDB using ADIT or ADITBeta.
Structure checks may be run using the Validation Server. Structures may be deposited to the PDB using ADIT.
Structure checks may be run using the Validation Server.

Occasionally users will experience difficulties proceeding through the precheck, validation or deposition steps of ADIT. The error message received is generally:

We're sorry, but an unanticipated error has occurred while trying to read your file. Please email what you were doing (precheck, validation, or deposit) with your file attached to deposit@deposit.rcsb.org and we will fix this situation as soon as possible. We apologize for the delay.

Usually this message is the result of format problems with the uploaded file(s). Some common problems and their potential solutions are given below.

Space group | Structure factor file | SEQRES Non-amino acid/Non-nucleic acid
SEQRES mismatches | CONECT records and MASTER cards in NMR | CNS mmCIF files

Space group

The space group in the CRYST1 card should be spaced out with no additional punctuation. For example:

Incorrect:

CRYST1   85.865   75.338  114.352  90.00  90.00 120.00 P6(5)22 

Correct:

CRYST1   85.865   75.338  114.352  90.00  90.00 120.00 P 65 2 2

The coordinate file can be re-loaded after this is corrected.

Structure factor file size

If a very large structure factor file is uploaded, the Validation Server may produce the above error message.

Large structure factor files should be compressed (resulting in a .Z extension) or gzipped (resulting in a .gz extension) and then uploaded into the Validation Server.

Please note that the validation checks can only be run on structure factor files in mmCIF format. Click here for more information on mmCIF structure factor files.

Non-amino acid/Non-nucleic acid residues in SEQRES records

SEQRES records (if given; these records can be generated automatically during the annotation process) should contain only the amino acid or nucleic acid sequence of the macromolecule that was studied. Ligands and water molecules should not be included. For example:

Incorrect:

SEQRES   1 A 130   ALA LEU GLU GLU LEU HIS TYR VAL PRO GLU GLY VAL LEU
SEQRES   2 A 130   HIS ARG ARG GLY PRO VAL ALA TYR LYS ILE PRO ARG PHE
SEQRES   3 A 130   GLY VAL ILE PRO ALA GLU PHE ARG VAL VAL LEU LEU ARG
SEQRES   4 A 130   ASP CYS PRO ASN LYS LYS ARG ILE TYR ARG VAL LYS ALA
SEQRES   5 A 130   VAL GLY GLU PRO PRO LEU PHE LEU GLY ARG VAL VAL PHE
SEQRES   6 A 130   PHE ALA ILE LYS ASP GLU ILE ARG GLU GLU ARG ALA GLN
SEQRES   7 A 130   HIS ALA ASN ASN ASN ALA LYS GLU LEU PHE ARG LEU ASP
SEQRES   8 A 130   VAL PRO THR THR PRO GLU LYS ILE ARG ASN THR CYS VAL
SEQRES   9 A 130   ASP LYS PHE ALA ALA TRS STA SAD SAD SAL SO4 H2O H2O
SEQRES  10 A 130   H2O H2O H2O H2O H2O

Correct:

SEQRES   1 A 109   ALA LEU GLU GLU LEU HIS TYR VAL PRO GLU GLY VAL LEU
SEQRES   2 A 109   HIS ARG ARG GLY PRO VAL ALA TYR LYS ILE PRO ARG PHE
SEQRES   3 A 109   GLY VAL ILE PRO ALA GLU PHE ARG VAL VAL LEU LEU ARG
SEQRES   4 A 109   ASP CYS PRO ASN LYS LYS ARG ILE TYR ARG VAL LYS ALA
SEQRES   5 A 109   VAL GLY GLU PRO PRO LEU PHE LEU GLY ARG VAL VAL PHE
SEQRES   6 A 109   PHE ALA ILE LYS ASP GLU ILE ARG GLU GLU ARG ALA GLN
SEQRES   7 A 109   HIS ALA ASN ASN ASN ALA LYS GLU LEU PHE ARG LEU ASP
SEQRES   8 A 109   VAL PRO THR THR PRO GLU LYS ILE ARG ASN THR CYS VAL
SEQRES   9 A 109   ASP LYS PHE ALA ALA

To correct the problem, non-amino acid and non-nucleic acid residues can be removed from the SEQRES records or the entire SEQRES section can be deleted. The coordinate file can then be re-loaded. Note: if the SEQRES records are deleted, the complete sequence of the molecule studied should be entered in ADIT during deposition.

Mismatches of chain ID's between the SEQRES records and the coordinate records

In the following example, the chain ID is given as "A" in the SEQRES records, but as X in the coordinate records (column 22).

SEQRES   1 A  52   THR ALA GLU GLU LEU HIS TYR VAL PRO GLU GLY VAL LEU
SEQRES   2 A  52   HIS ARG ARG GLY PRO VAL ALA TYR LYS ILE PRO ARG PHE
SEQRES   3 A  52   GLY VAL ILE PRO ALA GLU PHE ARG VAL VAL LEU LEU ARG
SEQRES   4 A  52   ASP CYS PRO ASN LYS LYS ARG ILE TYR ARG VAL LYS ALA
(snip)
ATOM      2  OG1 THR X   1       6.477  70.386 108.129  1.00 99.26      A
ATOM      3  CG2 THR X   1       7.152  70.135 110.434  1.00 96.21      A
ATOM      4  C   THR X   1       6.642  67.628 108.673  1.00 92.47      A
ATOM      5  O   THR X   1       7.782  68.064 108.501  1.00 91.91      A
ATOM      6  N   THR X   1       5.235  67.969 110.719  1.00 95.78      A
ATOM      7  CA  THR X   1       5.568  68.474 109.360  1.00 94.91      A
ATOM      8  N   ALA X   2       6.267  66.408 108.289  1.00 84.72      A
ATOM      9  CA  ALA X   2       7.168  65.487 107.604  1.00 72.54      A
ATOM     10  CB  ALA X   2       7.402  64.252 108.456  1.00 74.32      A
ATOM     11  C   ALA X   2       6.557  65.095 106.260  1.00 64.74      A
ATOM     12  O   ALA X   2       5.339  64.921 106.143  1.00 54.67      A
(snip)

Mismatches in other records (such as LINK, HELIX, or SHEET) can result in similar difficulties. To correct the problem, either the chain ID's can be edited in all relevant records or the SEQRES and/or other sections can be deleted. The coordinate file can then be reloaded. Note: if the SEQRES records are deleted, the complete sequence of the molecule studied should be entered in ADIT during deposition.

CONECT records and MASTER cards in NMR coordinate files should appear only (if at all) at the end of the final model and not after each model

These records do not need to be included and will be generated automatically as part of the annotation process. After deleting these records the edited coordinate file can be re-loaded.

CNS mmCIF files

If CNS is used to create an mmCIF file and the molecular description is left blank, the entity and struct_asym categories in the resulting mmCIF file will not contain any data. This produces an mmCIF syntax error, which gives an error in Precheck and in the 'Chemical/Biological Features' category of the ADIT deposition. Removing the entity and struct_asym categories from the mmCIF file and uploading the file into ADIT again will resolve the trouble. The corresponding information can then be entered in ADIT.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.