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| Submission Rules and Format |
Predictions in CASP17 for large structures may be submitted in a mmCIF format
Records in PDB like CASP format have the following equivalents in CASP mmCIF:
PARENT record
The PARENT record is no longer required, if you wish to include the information about a template structure it is advised to follow ModelCIF specifications.
See:
https://github.com/ihmwg/ModelCIF/blob/master/dictionary_documentation/documentation.md#adding-template-structures
- REMARK
_casp.remark "Some comment"
- METHOD
_casp.method "Description of the method"
- AUTHOR (mandatory)
_casp.author XXXX-XXXX-XXXX
TARGET (mandatory)
_casp.target TXXXX
preferably in sync with data block identifier
data_TXXXX
PFRMAT (mandatory)
_casp.pfrmat TS - STOICH (TS category, optionally). Predicted stoichiometry of an assembly target (in the form AiBjCn))
loop_
_casp_stoich.model_num
_casp_stoich.stoich
model_num1 AiBjCk
model_num2 AxByCz
- SCORE (for the TS category, optional, reliability of the model)
loop_
_casp_score.model_num
_casp_score.score
model_num1 score
model_num2 score"
- QSCORE (TS category, optional. Reliability of the interfaces in the quaternary structure of the model)
#
loop_
_casp_qscore.model_num
_casp_qscore.interface
_casp_qscore.score
model_num1 interface score
model_num2 interface score
- MODEL
Place model information within each record of _atom_site loop
_atom_site.pdbx_PDB_modelnum (within the atom coordinates loop)
```
- Chains and residue numbers
- Chains identifiers should be placed in:
_atom_site.auth_asym_id
Note: the values in _atom_site.label_asym_id will not be used during verification of the chains
- Residue numbers in:
_atom_site.auth_seq_id
not in _atom_site.label_seq_id
# casp_mmCIF_extenstions
data_casp_extensions.dict
_dictionary.title "CASP (predictioncenter.org) experiment metadata dictionary"
_dictionary.version 1.0.1
_dictionary.datablock_id casp_extensions.dict
###########################
## Category: casp
###########################
save_casp
_category.id casp
_category.mandatory_code no
_category_key.name '_casp.target'
_category.description.text
;
Category for CASP experiment specific metadata.
;
save_
###########################
## Atributes (Items)
###########################
save__casp.pfrmat
_item.name '_casp.pfrmat'
_item.category_id casp
_item.mandatory_code yes
_item_type.code code
_item_description.description "Model format (TS for Tertiary Structure)."
loop_
_item_enumeration.value
_item_enumeration.detail
"TS" "Tertiary Structure"
"QA" "Quality Assessment"
save_
save__casp.target
_item.name '_casp.target'
_item.category_id casp
_item.mandatory_code yes
_item_type.code code
_item_description.description "Target identifier (eg. T0999)."
save_
save__casp.author
_item.name '_casp.author'
_item.category_id casp
_item.mandatory_code no
_item_type.code line
_item_description.description "CASP AUTHOR ID /PIN (XXXX-XXXX-XXXX)."
save_
save__casp.remark
_item.name '_casp.remark'
_item.category_id casp
_item.mandatory_code no
_item_type.code text
_item_description.description "Additional remarks about model"
save_
save__casp.stoich
_item.name '_casp.stoich'
_item.category_id casp
_item.mandatory_code no
_item_type.code line
_item_description.description "TS category, optional. Predicted stoichiometry of an assembly target (in the form AiBjCn)"
save_
save__casp.method
_item.name '_casp.method'
_item.category_id casp
_item.mandatory_code no
_item_type.code line
_item_description.description "Method description"
save_
# ------------------------------------------------------------------------------
# Definition of _casp_qscore category
# ------------------------------------------------------------------------------
save_casp_qscore
_category.description
;
Q-score for CASP model and interface
;
_category.id casp_qscore
_category.mandatory_code no
loop_
_category_key.name '_casp_qscore.model_num'
'_casp_qscore.interface'
save_
# ------------------------------------------------------------------------------
# Attributes (Items) within _casp_qscore category
# ------------------------------------------------------------------------------
save_casp_qscore.model_num
_item_description.description "Model number"
_item.name '_casp_qscore.model_num'
_item.category_id casp_qscore
_item.mandatory_code yes
_item_type.code int
save_
save_casp_qscore.interface
_item_description.description "Interface definition - pairs of chains (e.g. AB)."
_item.name '_casp_qscore.interface'
_item.category_id casp_qscore
_item.mandatory_code yes
_item_type.code text
save_
save_casp_qscore.score
_item_description.description "Q-score for the model"
_item.name '_casp_qscore.score'
_item.category_id casp_qscore
_item.mandatory_code yes
_item_type.code float
save_
# ------------------------------------------------------------------------------
# Definition of _casp_score category
# ------------------------------------------------------------------------------
save_casp_score
_category.description
;
Score for CASP model
;
_category.id casp_score
_category.mandatory_code no
loop_
_category_key.name '_casp_score.model_num'
save_
# ------------------------------------------------------------------------------
# Attributes (Items)
# ------------------------------------------------------------------------------
save_casp_score.model_num
_item_description.description "Model number"
_item.name '_casp_score.model_num'
_item.category_id casp_score
_item.mandatory_code yes
_item_type.code int
save_
save_casp_score.score
_item_description.description "Score for the model"
_item.name '_casp_score.score'
_item.category_id casp_score
_item.mandatory_code yes
_item_type.code float
save_
# ------------------------------------------------------------------------------
# Definition of _casp_stoich category
# ------------------------------------------------------------------------------
save_casp_stoich
_category.description
;
Stoichiometry of CASP model
;
_category.id casp_stoich
_category.mandatory_code no
loop_
_category_key.name '_casp_stoich.model_num'
save_
# ------------------------------------------------------------------------------
# Attributes (Items)
# ------------------------------------------------------------------------------
save_casp_stoich.model_num
_item_description.description "Model number"
_item.name '_casp_stoich.model_num'
_item.category_id casp_stoich
_item.mandatory_code yes
_item_type.code int
save_
save_casp_stoich.stoich
_item_description.description "Stoichiometry of the model"
_item.name '_casp_stoich.stoich'
_item.category_id casp_score
_item.mandatory_code yes
_item_type.code float
save_
Example of CASP models in mmCIF
data_T0999
loop_
_audit_conform.dict_name
_audit_conform.dict_version
_audit_conform.dict_location
mmcif_pdbx.dic 5.367 http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
casp.dic 1.0.0 ./casp.dic
#
_casp.method "Method description"
_casp.pfrmat TS
_casp.remark "General remarks"
_casp.author 1234-5678-0000
_casp.target T0999
_casp.stoich A1B1
loop_
_casp_score.model_num
_casp_score.score
1 1.0
2 0.8
#
#_entry_id T0999
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . GLU A ? 1 ? 10.982 -9.774 1.377 1.0 90.0 1 A 1
ATOM 2 C CA . GLU A ? 1 ? 9.623 -9.833 1.984 1.0 85.5 1 A 1
ATOM 3 C C . GLU A ? 1 ? 8.913 -11.104 1.521 1.0 85.5 1 A 1
ATOM 4 O O . GLU A ? 1 ? 9.187 -11.630 0.461 1.0 80.0 1 A 1
ATOM 5 C CB . GLU A ? 1 ? 8.814 -8.614 1.546 1.0 85.45 1 A 1
ATOM 6 C CG . GLU A ? 1 ? 7.372 -8.754 2.039 1.0 75.0 1 A 1
ATOM 7 C CD . GLU A ? 1 ? 7.339 -8.625 3.562 1.0 93.5 1 A 1
ATOM 8 O OE1 . GLU A ? 1 ? 8.370 -8.307 4.131 1.0 90.5 1 A 1
ATOM 9 O OE2 . GLU A ? 1 ? 6.284 -8.846 4.132 1.0 85.4 1 A 1
ATOM 10 N N . THR A ? 2 ? 7.998 -11.599 2.304 1.0 70.6 2 A 1
ATOM 11 C CA . THR A ? 2 ? 7.266 -12.832 1.907 1.0 75.6 2 A 1
ATOM 12 C C . THR A ? 2 ? 6.096 -12.456 1.005 1.0 76.4 2 A 1
ATOM 13 O O . THR A ? 2 ? 5.008 -12.217 1.466 1.0 75.6 2 A 1
ATOM 14 C CB . THR A ? 2 ? 6.731 -13.533 3.157 1.0 70.9 2 A 1
ATOM 15 O OG1 . THR A ? 2 ? 7.662 -13.379 4.220 1.0 80.6 2 A 1
ATOM 16 C CG2 . THR A ? 2 ? 6.526 -15.019 2.864 1.0 83.46 2 A 1
ATOM 17 N N . VAL A ? 3 ? 6.308 -12.396 -0.278 1.0 50.7 3 A 1
ATOM 18 C CA . VAL A ? 3 ? 5.190 -12.030 -1.187 1.0 45.6 3 A 1
ATOM 19 C C . VAL A ? 3 ? 3.954 -12.870 -0.844 1.0 59.7 3 A 1
ATOM 20 O O . VAL A ? 3 ? 2.834 -12.471 -1.090 1.0 47.3 3 A 1
ATOM 21 C CB . VAL A ? 3 ? 5.608 -12.274 -2.641 1.0 44.0 3 A 1
ATOM 22 C CG1 . VAL A ? 3 ? 5.542 -13.771 -2.959 1.0 30.7 3 A 1
ATOM 23 C CG2 . VAL A ? 3 ? 4.664 -11.514 -3.573 1.0 40.35 3 A 1
ATOM 24 N N . GLU A ? 5 ? 4.146 -14.029 -0.272 1.0 80.7 5 A 1
ATOM 25 C CA . GLU A ? 5 ? 2.976 -14.882 0.086 1.0 83.6 5 A 1
ATOM 26 C C . GLU A ? 5 ? 2.153 -14.190 1.175 1.0 80.5 5 A 1
ATOM 27 O O . GLU A ? 5 ? 0.942 -14.141 1.109 1.0 85.4 5 A 1
ATOM 28 C CB . GLU A ? 5 ? 3.465 -16.238 0.597 1.0 87.55 5 A 1
ATOM 29 C CG . GLU A ? 5 ? 2.336 -17.264 0.479 1.0 81.2 5 A 1
ATOM 30 C CD . GLU A ? 5 ? 2.929 -18.671 0.391 1.0 70.1 5 A 1
ATOM 31 O OE1 . GLU A ? 5 ? 4.056 -18.846 0.823 1.0 77.75 5 A 1
ATOM 32 O OE2 . GLU A ? 5 ? 2.246 -19.551 -0.108 1.0 80.9 5 A 1
ATOM 33 N N . GLU A ? 1 ? 10.982 -9.774 1.377 1.0 90.0 1 A 2
ATOM 34 C CA . GLU A ? 1 ? 9.623 -9.833 1.984 1.0 85.5 1 A 2
ATOM 35 C C . GLU A ? 1 ? 8.913 -11.104 1.521 1.0 85.5 1 A 2
ATOM 36 O O . GLU A ? 1 ? 9.187 -11.630 0.461 1.0 80.0 1 A 2
ATOM 37 C CB . GLU A ? 1 ? 8.814 -8.614 1.546 1.0 85.45 1 A 2
ATOM 38 C CG . GLU A ? 1 ? 7.372 -8.754 2.039 1.0 75.0 1 A 2
ATOM 39 C CD . GLU A ? 1 ? 7.339 -8.625 3.562 1.0 93.5 1 A 2
ATOM 40 O OE1 . GLU A ? 1 ? 8.370 -8.307 4.131 1.0 90.5 1 A 2
ATOM 41 O OE2 . GLU A ? 1 ? 6.284 -8.846 4.132 1.0 85.4 1 A 2
ATOM 42 N N . THR A ? 2 ? 7.998 -11.599 2.304 1.0 70.6 2 A 2
ATOM 43 C CA . THR A ? 2 ? 7.266 -12.832 1.907 1.0 75.6 2 A 2
ATOM 44 C C . THR A ? 2 ? 6.096 -12.456 1.005 1.0 76.4 2 A 2
ATOM 45 O O . THR A ? 2 ? 5.008 -12.217 1.466 1.0 75.6 2 A 2
ATOM 46 C CB . THR A ? 2 ? 6.731 -13.533 3.157 1.0 70.9 2 A 2
ATOM 47 O OG1 . THR A ? 2 ? 7.662 -13.379 4.220 1.0 80.6 2 A 2
ATOM 48 C CG2 . THR A ? 2 ? 6.526 -15.019 2.864 1.0 83.46 2 A 2
ATOM 49 N N . VAL A ? 3 ? 6.308 -12.396 -0.278 1.0 50.7 3 A 2
ATOM 50 C CA . VAL A ? 3 ? 5.190 -12.030 -1.187 1.0 45.6 3 A 2
ATOM 51 C C . VAL A ? 3 ? 3.954 -12.870 -0.844 1.0 59.7 3 A 2
ATOM 52 O O . VAL A ? 3 ? 2.834 -12.471 -1.090 1.0 47.3 3 A 2
ATOM 53 C CB . VAL A ? 3 ? 5.608 -12.274 -2.641 1.0 44.0 3 A 2
ATOM 54 C CG1 . VAL A ? 3 ? 5.542 -13.771 -2.959 1.0 30.7 3 A 2
ATOM 55 C CG2 . VAL A ? 3 ? 4.664 -11.514 -3.573 1.0 40.35 3 A 2
ATOM 56 N N . GLU A ? 4 ? 4.146 -14.029 -0.272 1.0 80.7 4 A 2
ATOM 57 C CA . GLU A ? 4 ? 2.976 -14.882 0.086 1.0 83.6 4 A 2
ATOM 58 C C . GLU A ? 4 ? 2.153 -14.190 1.175 1.0 80.5 4 A 2
ATOM 59 O O . GLU A ? 4 ? 0.942 -14.141 1.109 1.0 85.4 4 A 2
ATOM 60 C CB . GLU A ? 4 ? 3.465 -16.238 0.597 1.0 87.55 4 A 2
ATOM 61 C CG . GLU A ? 4 ? 2.336 -17.264 0.479 1.0 81.2 4 A 2
ATOM 62 C CD . GLU A ? 4 ? 2.929 -18.671 0.391 1.0 70.1 4 A 2
ATOM 63 O OE1 . GLU A ? 4 ? 4.056 -18.846 0.823 1.0 77.75 4 A 2
ATOM 64 O OE2 . GLU A ? 4 ? 2.246 -19.551 -0.108 1.0 80.9 4 A 2
#
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