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Module for creating PDB records.
This module currently used the PDB format version 3.30 from July, 2011 http://www.wwpdb.org/documentation/format33/v3.3.html.
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Imports: wrap, RelaxError
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Auxiliary function for handling values of None.
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Auxiliary function for handling text values. This will convert None to empty strings and make sure everything is capitalised.
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Check that the record is ok.
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Generate the ATOM record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect9.html#ATOM. ATOMOverviewThe ATOM records present the atomic coordinates for standard amino acids and nucleotides. They also present the occupancy and temperature factor for each atom. Non-polymer chemical coordinates use the HETATM record type. The element symbol is always present on each ATOM record; charge is optional. Changes in ATOM/HETATM records result from the standardization atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary (ftp://ftp.wwpdb.org/pub/pdb/data/monomers). Record FormatThe format is: __________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|________________________________________________| | | | | | | 1 - 6 | Record name | "ATOM" | | | 7 - 11 | Integer | serial | Atom serial number. | | 13 - 16 | Atom | name | Atom name. | | 17 | Character | altLoc | Alternate location indicator. | | 18 - 20 | Residue name | resName | Residue name. | | 22 | Character | chainID | Chain identifier. | | 23 - 26 | Integer | resSeq | Residue sequence number. | | 27 | AChar | iCode | Code for insertion of residues. | | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. | | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. | | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. | | 55 - 60 | Real(6.2) | occupancy | Occupancy. | | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. | | 77 - 78 | LString(2) | element | Element symbol, right-justified. | | 79 - 80 | LString(2) | charge | Charge on the atom. | |_________|______________|______________|________________________________________________| DetailsATOM records for proteins are listed from amino to carboxyl terminus. Nucleic acid residues are listed from the 5' to the 3' terminus. Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13. Atom nomenclature begins with atom type. No ordering is specified for polysaccharides. Non-blank alphanumerical character is used for chain identifier. The list of ATOM records in a chain is terminated by a TER record. If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records. AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples). For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
Alphabet letters are commonly used for insertion code. The insertion code is used when two residues have the same numbering. The combination of residue numbering and insertion code defines the unique residue. If the depositor provides the data, then the isotropic B value is given for the temperature factor. If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor. Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases, these are blank. For refinements with program REFMAC prior 5.5.0042 which use TLS refinement, the values of B may include only the TLS contribution to the isotropic temperature factor rather than the full isotropic value. Verification/Validation/Value Authority ControlThe ATOM/HETATM records are checked for PDB file format, sequence information, and packing. Relationships to Other Record TypesThe ATOM records are compared to the corresponding sequence database. Sequence discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N
ATOM 33 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
ATOM 34 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
ATOM 35 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
ATOM 36 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
ATOM 37 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
ATOM 38 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
ATOM 39 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
ATOM 40 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
ATOM 41 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
ATOM 42 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
ATOM 43 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
ATOM 44 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
ATOM 45 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
ATOM 46 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
ATOM 47 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
ATOM 48 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
ATOM 49 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
ATOM 50 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
ATOM 51 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N
ATOM 52 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N
Example 2:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N
ATOM 33 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
ATOM 34 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
ATOM 35 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
ATOM 36 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
ATOM 37 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
ATOM 38 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
ATOM 39 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
ATOM 40 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
ATOM 41 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
ATOM 42 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N
ATOM 43 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
ATOM 44 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
ATOM 45 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
ATOM 46 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
ATOM 47 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
ATOM 48 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
ATOM 49 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
ATOM 50 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
ATOM 51 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
ATOM 52 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N
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Generate the CONECT record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect10.html#CONECT. CONECTOverviewThe CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as shown in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table. These records are generated automatically. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "CONECT" | | | 7 - 11 | Integer | serial | Atom serial number | | 12 - 16 | Integer | serial | Serial number of bonded atom | | 17 - 21 | Integer | serial | Serial number of bonded atom | | 22 - 26 | Integer | serial | Serial number of bonded atom | | 27 - 31 | Integer | serial | Serial number of bonded atom | |_________|______________|______________|____________________________________________________| DetailsCONECT records are present for:
No differentiation is made between atoms with delocalized charges (excess negative or positive charge). Atoms specified in the CONECT records have the same numbers as given in the coordinate section. All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record. If more than four fields are required for non-hydrogen and non-salt bridges, a second CONECT record with the same atom serial number in columns 7 - 11 will be used. These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order. The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11. For hydrogen bonds, when the hydrogen atom is present in the coordinates, a CONECT record between the hydrogen atom and its acceptor atom is generated. For NMR entries, CONECT records for one model are generated describing heterogen connectivity and others for LINK records assuming that all models are homogeneous models. Verification/Validation/Value Authority ControlConnectivity is checked for unusual bond lengths. Relationships to Other Record TypesCONECT records must be present in an entry that contains either non-standard groups or disulfide bonds. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
CONECT 1179 746 1184 1195 1203
CONECT 1179 1211 1222
CONECT 1021 544 1017 1020 1022
Known ProblemsCONECT records involving atoms for which the coordinates are not present in the entry (e.g., symmetry-generated) are not given. CONECT records involving atoms for which the coordinates are missing due to disorder, are also not provided.
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Generate the END record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect11.html#END. ENDOverviewThe END record marks the end of the PDB file. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "END " | | |_________|______________|______________|____________________________________________________| DetailsEND is the final record of a coordinate entry. Verification/Validation/Value Authority ControlEND must appear in every coordinate entry. Relationships to Other Record TypesThis is the final record in the entry. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
END
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Generate the ENDMDL record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/v3.3.html. ENDMDLOverviewThe ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "ENDMDL" | | |_________|______________|______________|____________________________________________________| DetailsMODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries. All the models in a multi-model entry must represent the same structure. Every MODEL record has an associated ENDMDL record. Verification/Validation/Value Authority ControlEntries with multiple structures in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models. Relationships to Other Record TypesThere must be a corresponding MODEL record. In the case of an NMR entry, the NUMMDL record states the number of model structures that are present in the individual entry. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
...
...
ATOM 14550 1HG GLU 122 -14.364 14.787 -14.258 1.00 0.00 H
ATOM 14551 2HG GLU 122 -13.794 13.738 -12.961 1.00 0.00 H
TER 14552 GLU 122
ENDMDL
MODEL 9
ATOM 14553 N SER 1 -28.280 1.567 12.004 1.00 0.00 N
ATOM 14554 CA SER 1 -27.749 0.392 11.256 1.00 0.00 C
...
...
ATOM 16369 1HG GLU 122 -3.757 18.546 -8.439 1.00 0.00 H
ATOM 16370 2HG GLU 122 -3.066 17.166 -7.584 1.00 0.00 H
TER 16371 GLU 122
ENDMDL
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Generate the FORMUL record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect4.html#FORMUL. FORMULOverviewThe FORMUL record presents the chemical formula and charge of a non-standard group. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "FORMUL" | | | 9 - 10 | Integer | compNum | Component number. | | 13 - 15 | LString(3) | hetID | Het identifier. | | 17 - 18 | Integer | continuation | Continuation number. | | 19 | Character | asterisk | "*" for water. | | 20 - 70 | String | text | Chemical formula. | |_________|______________|______________|____________________________________________________| DetailsThe elements of the chemical formula are given in the order following Hill ordering. The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. The number of each atom type present immediately follows its chemical symbol without an intervening blank space. There will be no number indicated if there is only one atom for a particular atom type. Each set of SEQRES records and each HET group is assigned a component number in an entry. These numbers are assigned serially, beginning with 1 for the first set of SEQRES records. In addition:
All occurrences of the HET group within a chain are grouped together with a multiplier. The remaining occurrences are also grouped with a multiplier. The sum of the multipliers is the number equaling the number of times that that HET group appears in the entry. A continuation field is provided in the event that more space is needed for the formula. Columns 17 - 18 are used in order to maintain continuity with the existing format. Verification/Validation/Value Authority ControlFor each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. The FORMUL record is generated automatically by PDB processing programs using the het group template file and information from HETATM records. UNL, UNK and UNX will not be listed in FORMUL even though these het groups present in the coordinate section. Relationships to Other Record TypesFor each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
FORMUL 3 MG 2(MG 2+)
FORMUL 5 SO4 6(O4 S 2-)
FORMUL 13 HOH *360(H2 O)
FORMUL 3 NAP 2(C21 H28 N7 O17 P3)
FORMUL 4 FOL 2(C19 H19 N7 O6)
FORMUL 5 1PE C10 H22 O6
FORMUL 2 NX5 C14 H10 O2 CL2 S
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Generate the HELIX record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect5.html#HELIX. HELIXOverviewHELIX records are used to identify the position of helices in the molecule. Helices are named, numbered, and classified by type. The residues where the helix begins and ends are noted, as well as the total length. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "HELIX " | | | 8 - 10 | Integer | serNum | Serial number of the helix. This starts at 1 and | | | | | increases incrementally. | | 12 - 14 | LString(3) | helixID | Helix identifier. In addition to a serial number, | | | | | each helix is given an alphanumeric character | | | | | helix identifier. | | 16 - 18 | Residue name | initResName | Name of the initial residue. | | 20 | Character | initChainID | Chain identifier for the chain containing this | | | | | helix. | | 22 - 25 | Integer | initSeqNum | Sequence number of the initial residue. | | 26 | AChar | initICode | Insertion code of the initial residue. | | 28 - 30 | Residue name | endResName | Name of the terminal residue of the helix. | | 32 | Character | endChainID | Chain identifier for the chain containing this | | | | | helix. | | 34 - 37 | Integer | endSeqNum | Sequence number of the terminal residue. | | 38 | AChar | endICode | Insertion code of the terminal residue. | | 39 - 40 | Integer | helixClass | Helix class (see below). | | 41 - 70 | String | comment | Comment about this helix. | | 72 - 76 | Integer | length | Length of this helix. | |_________|______________|______________|____________________________________________________| DetailsAdditional HELIX records with different serial numbers and identifiers occur if more than one helix is present. The initial residue of the helix is the N-terminal residue. Helices are classified as follows: _____________________________________________________ | | CLASS NUMBER | | TYPE OF HELIX | (COLUMNS 39 - 40) | |_______________________________|___________________| | | | | Right-handed alpha (default) | 1 | | Right-handed omega | 2 | | Right-handed pi | 3 | | Right-handed gamma | 4 | | Right-handed 3 - 10 | 5 | | Left-handed alpha | 6 | | Left-handed omega | 7 | | Left-handed gamma | 8 | | 2 - 7 ribbon/helix | 9 | | Polyproline | 10 | |_______________________________|___________________| Relationships to Other Record TypesThere may be related information in the REMARKs. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
HELIX 1 HA GLY A 86 GLY A 94 1 9
HELIX 2 HB GLY B 86 GLY B 94 1 9
HELIX 21 21 PRO J 385 LEU J 388 5 4
HELIX 22 22 PHE J 397 PHE J 402 5 6
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Generate the HET record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect4.html#HET. HETOverviewHET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are not part of a biological polymer described in SEQRES and considered to be a molecule bound to the polymer, or they are a chemical species that constitute part of a biological polymer and is not one of the following:
HET records also describe chemical components for which the chemical identity is unknown, in which case the group is assigned the hetID UNL (Unknown Ligand). The heterogen section of a PDB formatted file contains the complete description of non-standard residues in the entry. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "HET " | | | 8 - 10 | LString(3) | hetID | Het identifier, right-justified. | | 13 | Character | ChainID | Chain identifier. | | 14 - 17 | Integer | seqNum | Sequence number. | | 18 | AChar | iCode | Insertion code. | | 21 - 25 | Integer | numHetAtoms | Number of HETATM records for the group present in | | | | | the entry. | | 31 - 70 | String | text | Text describing Het group. | |_________|______________|______________|____________________________________________________| DetailsEach HET group is assigned a hetID of not more than three (3) alphanumeric characters. The sequence number, chain identifier, insertion code, and number of coordinate records are given for each occurrence of the HET group in the entry. The chemical name of the HET group is given in the HETNAM record and synonyms for the chemical name are given in the HETSYN records, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers. There is a separate HET record for each occurrence of the HET group in an entry. A particular HET group is represented in the PDB archive with a unique hetID. PDB entries do not have HET records for water molecules, deuterated water, or methanol (when used as solvent). Unknown atoms or ions will be represented as UNX with the chemical formula X1. Unknown ligands are UNL; unknown amino acids are UNK. Verification/Validation/Value Authority ControlFor each het group that appears in the entry, the wwPDB checks that the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records appear, if applicable. The HET record is generated automatically using the Chemical Component Dictionary and information from the HETATM records. Each unique hetID represents a unique molecule. Relationships to Other Record TypesFor each het group that appears in the entry, there must be corresponding HET, HETNAM, HETSYN, FORMUL,HETATM, and CONECT records. LINK records may also be created. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
HET TRS B 975 8
HET UDP A1457 25
HET B3P A1458 19
HET NAG Y 3 15
HET FUC Y 4 10
HET NON Y 5 12
HET UNK A 161 1
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Generate the HETATM record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect9.html#HETATM. HETATMOverviewNon-polymer or other "non-standard" chemical coordinates, such as water molecules or atoms presented in HET groups use the HETATM record type. They also present the occupancy and temperature factor for each atom. The ATOM records present the atomic coordinates for standard residues. The element symbol is always present on each HETATM record; charge is optional. Changes in ATOM/HETATM records will require standardization in atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary, ftp://ftp.wwpdb.org/pub/pdb/data/monomers. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "HETATM" | | | 7 - 11 | Integer | serial | Atom serial number. | | 13 - 16 | Atom | name | Atom name. | | 17 | Character | altLoc | Alternate location indicator. | | 18 - 20 | Residue name | resName | Residue name. | | 22 | Character | chainID | Chain identifier. | | 23 - 26 | Integer | resSeq | Residue sequence number. | | 27 | AChar | iCode | Code for insertion of residues. | | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X. | | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y. | | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z. | | 55 - 60 | Real(6.2) | occupancy | Occupancy. | | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. | | 77 - 78 | LString(2) | element | Element symbol; right-justified. | | 79 - 80 | LString(2) | charge | Charge on the atom. | |_________|______________|______________|____________________________________________________| DetailsThe x, y, z coordinates are in Angstrom units. No ordering is specified for polysaccharides. See the HET section of this document regarding naming of heterogens. See the Chemical Component Dictionary for residue names, formulas, and topology of the HET groups that have appeared so far in the PDB (see ftp://ftp.wwpdb.org/pub/pdb/data/monomers). If the depositor provides the data, then the isotropic B value is given for the temperature factor. If there are neither isotropic B values provided by the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor. Insertion codes and element naming are fully described in the ATOM section of this document. Verification/Validation/Value Authority ControlProcessing programs check ATOM/HETATM records for PDB file format, sequence information, and packing. Relationships to Other Record TypesHETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 8237 MG MG A1001 13.872 -2.555 -29.045 1.00 27.36 MG
HETATM 3835 FE HEM A 1 17.140 3.115 15.066 1.00 14.14 FE
HETATM 8238 S SO4 A2001 10.885 -15.746 -14.404 1.00 47.84 S
HETATM 8239 O1 SO4 A2001 11.191 -14.833 -15.531 1.00 50.12 O
HETATM 8240 O2 SO4 A2001 9.576 -16.338 -14.706 1.00 48.55 O
HETATM 8241 O3 SO4 A2001 11.995 -16.703 -14.431 1.00 49.88 O
HETATM 8242 O4 SO4 A2001 10.932 -15.073 -13.100 1.00 49.91 O
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Generate the HETNAM record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect4.html#HETNAM. HETNAMOverviewThis record gives the chemical name of the compound with the given hetID. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "HETNAM" | | | 9 - 10 | Continuation | continuation | Allows concatenation of multiple records. | | 12 - 14 | LString(3) | hetID | Het identifier, right-justified. | | 16 - 70 | String | text | Chemical name. | |_________|______________|______________|____________________________________________________| DetailsEach hetID is assigned a unique chemical name for the HETNAM record, see ftp://ftp.wwpdb.org/pub/pdb/data/monomers. Other names for the group are given on HETSYN records. PDB entries follow IUPAC/IUB naming conventions to describe groups systematically. The special character "~" is used to indicate superscript in a heterogen name. For example: N6 will be listed in the HETNAM section as N~6~, with the ~ character indicating both the start and end of the superscript in the name, e.g.:
Continuation of chemical names onto subsequent records is allowed. Only one HETNAM record is included for a given hetID, even if the same hetID appears on more than one HET record. Verification/Validation/Value Authority ControlFor each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. The HETNAM record is generated automatically using the Chemical Component Dictionary and information from HETATM records. Relationships to Other Record TypesFor each het group that appears in the entry, there must be corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records. HETSYN and LINK records may also be created. ExampleExample 1:
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM SAD BETA-METHYLENE SELENAZOLE-4-CARBOXAMIDE ADENINE
HETNAM 2 SAD DINUCLEOTIDE
HETNAM UDP URIDINE-5'-DIPHOSPHATE
HETNAM UNX UNKNOWN ATOM OR ION
HETNAM UNL UNKNOWN LIGAND
HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-
HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
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Generate the MASTER record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect11.html#MASTER. MASTEROverviewThe MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types. MASTER records only the first model when there are multiple models in the coordinates. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "MASTER" | | | 11 - 15 | Integer | numRemark | Number of REMARK records | | 16 - 20 | Integer | "0" | | | 21 - 25 | Integer | numHet | Number of HET records | | 26 - 30 | Integer | numHelix | Number of HELIX records | | 31 - 35 | Integer | numSheet | Number of SHEET records | | 36 - 40 | Integer | numTurn | deprecated | | 41 - 45 | Integer | numSite | Number of SITE records | | 46 - 50 | Integer | numXform | Number of coordinate transformation records | | | | | (ORIGX+SCALE+MTRIX) | | 51 - 55 | Integer | numCoord | Number of atomic coordinate records (ATOM+HETATM) | | 56 - 60 | Integer | numTer | Number of TER records | | 61 - 65 | Integer | numConect | Number of CONECT records | | 66 - 70 | Integer | numSeq | Number of SEQRES records | |_________|______________|______________|____________________________________________________| DetailsMASTER gives checksums of the number of records in the entry, for selected record types. MASTER records only the first model when there are multiple models in the coordinates. Verification/Validation/Value Authority ControlThe MASTER line is automatically generated. Relationships to Other Record TypesMASTER presents a checksum of the lines present for each of the record types listed above. ExampleExample 1:
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MASTER 40 0 0 0 0 0 0 6 2930 2 0 29
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Generate the MODEL record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect9.html#MODEL. MODELOverviewThe MODEL record specifies the model serial number when multiple models of the same structure are presented in a single coordinate entry, as is often the case with structures determined by NMR. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "MODEL " | | | 11 - 14 | Integer | serial | Model serial number. | |_________|______________|______________|____________________________________________________| DetailsThis record is used only when more than one model appears in an entry. Generally, it is employed mainly for NMR structures. The chemical connectivity should be the same for each model. ATOM, HETATM, ANISOU, and TER records for each model structure and are interspersed as needed between MODEL and ENDMDL records. The numbering of models is sequential, beginning with 1. All models in a deposition should be superimposed in an appropriate author determined manner and only one superposition method should be used. Structures from different experiments, or different domains of a structure should not be superimposed and deposited as models of a deposition. All models in an NMR ensemble should be homogeneous - each model should have the exact same atoms (hydrogen and heavy atoms), sequence and chemistry. All models in an NMR entry should have hydrogen atoms. Deposition of minimized average structure must be accompanied with ensemble and must be homogeneous with ensemble. A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry cannot have more than 99,999 atoms. Entries that go beyond this atom limit must be split into multiple entries, each containing no more than the limits specified above. Verification/Validation/Value Authority ControlEntries with multiple models in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models. Relationships to Other Record TypesEach MODEL must have a corresponding ENDMDL record. ExamplesExample 1:
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MODEL 1
ATOM 1 N ALA A 1 11.104 6.134 -6.504 1.00 0.00 N
ATOM 2 CA ALA A 1 11.639 6.071 -5.147 1.00 0.00 C
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ATOM 293 1HG GLU A 18 -14.861 -4.847 0.361 1.00 0.00 H
ATOM 294 2HG GLU A 18 -13.518 -3.769 0.084 1.00 0.00 H
TER 295 GLU A 18
ENDMDL
MODEL 2
ATOM 296 N ALA A 1 10.883 6.779 -6.464 1.00 0.00 N
ATOM 297 CA ALA A 1 11.451 6.531 -5.142 1.00 0.00 C
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ATOM 588 1HG GLU A 18 -13.363 -4.163 -2.372 1.00 0.00 H
ATOM 589 2HG GLU A 18 -12.634 -3.023 -3.475 1.00 0.00 H
TER 590 GLU A 18
ENDMDL
Example 2:
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MODEL 1
ATOM 1 N AALA A 1 72.883 57.697 56.410 0.50 83.80 N
ATOM 2 CA AALA A 1 73.796 56.531 56.644 0.50 84.78 C
ATOM 3 C AALA A 1 74.549 56.551 57.997 0.50 85.05 C
ATOM 4 O AALA A 1 73.951 56.413 59.075 0.50 84.77 O
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HETATM37900 O AHOH 490 -24.915 147.513 36.413 0.50 41.86 O
HETATM37901 O AHOH 491 -28.699 130.471 22.248 0.50 36.06 O
HETATM37902 O AHOH 492 -33.309 184.488 26.176 0.50 15.00 O
ENDMDL
MODEL 2
ATOM 1 N BALA A 1 72.883 57.697 56.410 0.50 83.80 N
ATOM 2 CA BALA A 1 73.796 56.531 56.644 0.50 84.78 C
ATOM 3 C BALA A 1 74.549 56.551 57.997 0.50 85.05 C
ATOM 4 O BALA A 1 73.951 56.413 59.075 0.50 84.77 O
ATOM 5 CB BALA A 1 74.804 56.369 55.453 0.50 84.29 C
ATOM 6 N BASP A 2 75.872 56.703 57.905 0.50 85.59 N
ATOM 7 CA BASP A 2 76.801 56.651 59.048 0.50 85.67 C
ATOM 8 C BASP A 2 76.283 57.361 60.309 0.50 84.80 C
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Generate the REMARK record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/remarks.html. REMARKOverviewREMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database. The very first line of every set of REMARK records is used as a spacer to aid in reading: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|_____________|_____________|______________________________________________________| | | | | | | 1 - 6 | Record name | "REMARK" | | | 8 - 10 | Integer | remarkNum | Remark number. It is not an error for remark n to | | | | | exist in an entry when remark n-1 does not. | | 12 - 79 | LString | empty | Left as white space in first line of each new | | | | | remark. | |_________|_____________|_____________|______________________________________________________|
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Generate the SHEET record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect5.html#SHEET. SHEETOverviewSHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "SHEET " | | | 8 - 10 | Integer | strand | Strand number which starts at 1 for each strand | | | | | within a sheet and increases by one. | | 12 - 14 | LString(3) | sheetID | Sheet identifier. | | 15 - 16 | Integer | numStrands | Number of strands in sheet. | | 18 - 20 | Residue name | initResName | Residue name of initial residue. | | 22 | Character | initChainID | Chain identifier of initial residue in strand. | | 23 - 26 | Integer | initSeqNum | Sequence number of initial residue in strand. | | 27 | AChar | initICode | Insertion code of initial residue in strand. | | 29 - 31 | Residue name | endResName | Residue name of terminal residue. | | 33 | Character | endChainID | Chain identifier of terminal residue. | | 34 - 37 | Integer | endSeqNum | Sequence number of terminal residue. | | 38 | AChar | endICode | Insertion code of terminal residue. | | 39 - 40 | Integer | sense | Sense of strand with respect to previous strand in | | | | | the sheet. 0 if first strand, 1 if parallel, and | | | | | -1 if anti-parallel. | | 42 - 45 | Atom | curAtom | Registration. Atom name in current strand. | | 46 - 48 | Residue name | curResName | Registration. Residue name in current strand. | | 50 | Character | curChainId | Registration. Chain identifier in current strand. | | 51 - 54 | Integer | curResSeq | Registration. Residue sequence number in current | | | | | strand. | | 55 | AChar | curICode | Registration. Insertion code in current strand. | | 57 - 60 | Atom | prevAtom | Registration. Atom name in previous strand. | | 61 - 63 | Residue name | prevResName | Registration. Residue name in previous strand. | | 65 | Character | prevChainId | Registration. Chain identifier in previous strand.| | 66 - 69 | Integer | prevResSeq | Registration. Residue sequence number in previous | | | | | strand. | | 70 | AChar | prevICode | Registration. Insertion code in previous strand. | |_________|______________|______________|____________________________________________________| DetailsThe initial residue for a strand is its N-terminus. Strand registration information is provided in columns 39 - 70. Strands are listed starting with one edge of the sheet and continuing to the spatially adjacent strand. The sense in columns 39 - 40 indicates whether strand n is parallel (sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to zero (0) for the first strand of a sheet. The registration (columns 42 - 70) of strand n to strand n-1 may be specified by one hydrogen bond between each such pair of strands. This is done by providing the hydrogen bonding between the current and previous strands. No register information should be provided for the first strand. Split strands, or strands with two or more runs of residues from discontinuous parts of the amino acid sequence, are explicitly listed. Detail description can be included in the REMARK 700. Relationships to Other Record TypesIf the entry contains bifurcated sheets or beta-barrels, the relevant REMARK 700 records must be provided. See the REMARK section for details. ExamplesExample 1:
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SHEET 1 A 5 THR A 107 ARG A 110 0
SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107
SHEET 3 A 5 ARG A 87 SER A 91 -1 N LEU A 89 O TYR A 97
SHEET 4 A 5 TRP A 71 ASP A 75 -1 N ALA A 74 O ILE A 88
SHEET 5 A 5 GLY A 52 PHE A 56 -1 N PHE A 56 O TRP A 71
SHEET 1 B 5 THR B 107 ARG B 110 0
SHEET 2 B 5 ILE B 96 THR B 99 -1 N LYS B 98 O THR B 107
SHEET 3 B 5 ARG B 87 SER B 91 -1 N LEU B 89 O TYR B 97
SHEET 4 B 5 TRP B 71 ASP B 75 -1 N ALA B 74 O ILE B 88
SHEET 5 B 5 GLY B 52 ILE B 55 -1 N ASP B 54 O GLU B 73
The sheet presented as BS1 below is an eight-stranded beta-barrel. This is represented by a nine-stranded sheet in which the first and last strands are identical: SHEET 1 BS1 9 VAL 13 ILE 17 0 SHEET 2 BS1 9 ALA 70 ILE 73 1 O TRP 72 N ILE 17 SHEET 3 BS1 9 LYS 127 PHE 132 1 O ILE 129 N ILE 73 SHEET 4 BS1 9 GLY 221 ASP 225 1 O GLY 221 N ILE 130 SHEET 5 BS1 9 VAL 248 GLU 253 1 O PHE 249 N ILE 222 SHEET 6 BS1 9 LEU 276 ASP 278 1 N LEU 277 O GLY 252 SHEET 7 BS1 9 TYR 310 THR 318 1 O VAL 317 N ASP 278 SHEET 8 BS1 9 VAL 351 TYR 356 1 O VAL 351 N THR 318 SHEET 9 BS1 9 VAL 13 ILE 17 1 N VAL 14 O PRO 352 The sheet structure of this example is bifurcated. In order to represent this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are identical: SHEET 1 BS7 3 HIS 662 THR 665 0 SHEET 2 BS7 3 LYS 639 LYS 648 -1 N PHE 643 O HIS 662 SHEET 3 BS7 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646 SHEET 1 BS8 3 ASN 653 TRP 656 0 SHEET 2 BS8 3 LYS 639 LYS 648 -1 N LYS 647 O THR 655 SHEET 3 BS8 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646
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Generate the TER record. The following is the PDB v3.3 documentation http://www.wwpdb.org/documentation/format33/sect9.html#TER. TEROverviewThe TER record indicates the end of a list of ATOM/HETATM records for a chain. Record FormatThe format is: ______________________________________________________________________________________________ | | | | | | Columns | Data type | Field | Definition | |_________|______________|______________|____________________________________________________| | | | | | | 1 - 6 | Record name | "TER " | | | 7 - 11 | Integer | serial | Serial number. | | 18 - 20 | Residue name | resName | Residue name. | | 22 | Character | chainID | Chain identifier. | | 23 - 26 | Integer | resSeq | Residue sequence number. | | 27 | AChar | iCode | Insertion code. | |_________|______________|______________|____________________________________________________| DetailsEvery chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record. The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which there are determined coordinates. For proteins, the residue defined on the TER record is the carboxy-terminal residue; for nucleic acids it is the 3'-terminal residue. For a cyclic molecule, the choice of termini is arbitrary. Terminal oxygen atoms are presented as OXT for proteins, and as O5' or OP3 for nucleic acids. These atoms are present only if the last residue in the polymer is truly the last residue in the SEQRES. The TER record has the same residue name, chain identifier, sequence number and insertion code as the terminal residue. The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER. Verification/Validation/Value Authority ControlTER must appear at the terminal carboxyl end or 3' end of a chain. For proteins, there is usually a terminal oxygen, labeled OXT. The validation program checks for the occurrence of TER and OXT records. Relationships to Other Record TypesThe residue name appearing on the TER record must be the same as the residue name of the immediately preceding ATOM or non-water HETATM record. ExampleExample 1:
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ATOM 601 N LEU A 75 -17.070 -16.002 2.409 1.00 55.63 N
ATOM 602 CA LEU A 75 -16.343 -16.746 3.444 1.00 55.50 C
ATOM 603 C LEU A 75 -16.499 -18.263 3.300 1.00 55.55 C
ATOM 604 O LEU A 75 -16.645 -18.789 2.195 1.00 55.50 O
ATOM 605 CB LEU A 75 -16.776 -16.283 4.844 1.00 55.51 C
TER 606 LEU A 75
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ATOM 1185 O LEU B 75 26.292 -4.310 16.940 1.00 55.45 O
ATOM 1186 CB LEU B 75 23.881 -1.551 16.797 1.00 55.32 C
TER 1187 LEU B 75
HETATM 1188 H2 SRT A1076 -17.263 11.260 28.634 1.00 59.62 H
HETATM 1189 HA SRT A1076 -19.347 11.519 28.341 1.00 59.42 H
HETATM 1190 H3 SRT A1076 -17.157 14.303 28.677 1.00 58.00 H
HETATM 1191 HB SRT A1076 -15.110 13.610 28.816 1.00 57.77 H
HETATM 1192 O1 SRT A1076 -17.028 11.281 31.131 1.00 62.63 O
ATOM 295 HB2 ALA A 18 4.601 -9.393 7.275 1.00 0.00 H
ATOM 296 HB3 ALA A 18 3.340 -9.147 6.043 1.00 0.00 H
TER 297 ALA A 18
ENDMDL
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