ADIT Validation Server Home
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.
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 help@rcsb.rutgers.edu 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.