Introduction to Protein Data Bank Format

Protein Data Bank (PDB) format is a standard for files containing atomic coordinates. It is used for structures in the Protein Data Bank and is read and written by many programs. While this short description will suffice for many users, those in need of further details should consult the definitive description. The complete PDB file specification provides for a wealth of information, including authors, literature references, and the method of structure determination.

PDB format consists of lines of information in a text file. Each line of information in the file is called a record. A PDB file generally contains several different types of records, arranged in a specific order to describe a structure.

Selected Protein Data Bank Record Types
Record TypeData Provided by Record
ATOM atomic coordinate record containing the X,Y,Z orthogonal Å coordinates for atoms in standard residues (amino acids and nucleic acids).
HETATM atomic coordinate record containing the X,Y,Z orthogonal Å coordinates for atoms in nonstandard residues. Nonstandard residues include inhibitors, cofactors, ions, and solvent. The only functional difference from ATOM records is that HETATM residues are by default not connected to other residues. Note that water residues should be in HETATM records.
TER indicates the end of a chain of residues. For example, a hemoglobin molecule consists of four subunit chains that are not connected. TER indicates the end of a chain and prevents the display of a connection to the next chain.
HELIX indicates the location and type (right-handed alpha, etc.) of helices. One record per helix.
SHEET indicates the location, sense (anti-parallel, etc.) and registration with respect to the previous strand in the sheet (if any) of each strand in the model. One record per strand.
SSBOND defines disulfide bond linkages between cysteine residues.

The formats of these record types are given in the tables below. Older PDB files may not adhere completely to the specifications. Some differences between older and newer files occur in the fields following the temperature factor in ATOM and HETATM records; these fields are omitted from the examples. Some fields are frequently blank, such as the alternate location indicator when an atom does not have alternate locations.

Protein Data Bank Format:
Coordinate Section
Record TypeColumnsData JustificationData Type
ATOM 1-4“ATOM”character
7-11#Atom serial numberrightinteger
13-16Atom nameleft*character
17Alternate location indicatorcharacter
18-20§Residue namerightcharacter
22Chain identifiercharacter
23-26Residue sequence numberrightinteger
27Code for insertions of residuescharacter
31-38X orthogonal Å coordinaterightreal (8.3)
39-46Y orthogonal Å coordinaterightreal (8.3)
47-54Z orthogonal Å coordinaterightreal (8.3)
55-60Occupancyrightreal (6.2)
61-66Temperature factorrightreal (6.2)
73-76Segment identifierleftcharacter
77-78Element symbolrightcharacter
79-80Chargecharacter
HETATM1-6“HETATM”character
7-80same as ATOM records
TER 1-3“TER”character
7-11#Serial numberrightinteger
18-20§Residue namerightcharacter
22Chain identifiercharacter
23-26Residue sequence numberrightinteger
27Code for insertions of residuescharacter

#Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records, and in TER records, only the “TER” is required.

*Atom names start with element symbols right-justified in columns 13-14 as permitted by the length of the name. For example, the symbol FE for iron appears in columns 13-14, whereas the symbol C for carbon appears in column 14 (see Misaligned Atom Names). If an atom name has four characters, however, it must start in column 13 even if the element symbol is a single character (for example, see Hydrogen Atoms).

§Chimera allows (nonstandard) use of four-character residue names occupying an additional column to the right.

Segment identifier is obsolete, but still used by some programs. Chimera assigns it as the atom attribute pdbSegment to allow command-line specification.

Protein Data Bank Format:
Protein Secondary Structure and Disulfides
Record TypeColumnsData JustificationData Type
HELIX 1-5“HELIX”character
8-10Helix serial numberrightinteger
12-14Helix identifierrightcharacter
16-18§Initial residue namerightcharacter
20Chain identifiercharacter
22-25Residue sequence numberrightinteger
26Code for insertions of residuescharacter
28-30§Terminal residue namerightcharacter
32Chain identifiercharacter
34-37Residue sequence numberrightinteger
38Code for insertions of residuescharacter
39-40Type of helixrightinteger
41-70Commentleftcharacter
72-76Length of helixrightinteger
SHEET 1-5“SHEET”character
8-10Strand number (in current sheet)rightinteger
12-14Sheet identifierrightcharacter
15-16Number of strands (in current sheet)rightinteger
18-20§Initial residue namerightcharacter
22Chain identifiercharacter
23-26Residue sequence numberrightinteger
27Code for insertions of residuescharacter
29-31§Terminal residue namerightcharacter
33Chain identifiercharacter
34-37Residue sequence numberrightinteger
38Code for insertions of residuescharacter
39-40Strand sense with respect to previousrightinteger

The following fields identify two atoms involved in a hydrogen bond,
the first in the current strand and the second in the previous strand.
These fields should be blank for strand 1 (the first strand in a sheet).

42-45Atom name (as per ATOM record)leftcharacter
46-48§Residue namerightcharacter
50Chain identifiercharacter
51-54Residue sequence numberrightinteger
55Code for insertions of residuescharacter
57-60Atom name (as per ATOM record)leftcharacter
61-63§Residue namerightcharacter
65Chain identifiercharacter
66-69Residue sequence numberrightinteger
70Code for insertions of residuescharacter
SSBOND 1-6“SSBOND”character
8-10Serial numberrightinteger
12-14Residue name (“CYS”)rightcharacter
16Chain identifiercharacter
18-21Residue sequence numberrightinteger
22Code for insertions of residuescharacter
26-28Residue name (“CYS”)rightcharacter
30Chain identifiercharacter
32-35Residue sequence numberrightinteger
36Code for insertions of residuescharacter
60-65Symmetry operator for first residuerightinteger
67-72Symmetry operator for second residuerightinteger
74-78Length of disulfide bondrightreal (5.2)

Helix types:
1Right-handed alpha (default) 6Left-handed alpha
2Right-handed omega 7Left-handed omega
3Right-handed pi 8Left-handed gamma
4Right-handed gamma 92/7 ribbon/helix
5Right-handed 3/10 10Polyproline

Sense is 0 for strand 1 (the first strand in a sheet), 1 for parallel, and –1 for antiparallel.

For those who are familiar with the FORTRAN programming language, the following format descriptions will be meaningful. Those unfamiliar with FORTRAN should ignore this gibberish:
ATOM
HETATM
Format ( A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,10X,A2,A2 )
HELIX Format ( A6,1X,I3,1X,A3,2(1X,A3,1X,A1,1X,I4,A1),I2,A30,1X,I5 )
SHEET Format ( A6,1X,I3,1X,A3,I2,2(1X,A3,1X,A1,I4,A1),I2,2(1X,A4,A3,1X,A1,I4,A1) )
SSBOND Format ( A6,1X,I3,1X,A3,1X,A1,1X,I4,A1,3X,A3,1X,A1,1X,I4,A1,23X,2(2I3,1X),F5.2 )

Examples of PDB Format

Glucagon is a small protein of 29 amino acids in a single chain. The first residue is the amino-terminal amino acid, histidine, which is followed by a serine residue and then a glutamine. The coordinate information (entry 1gcn) starts with:

ATOM      1  N   HIS A   1      49.668  24.248  10.436  1.00 25.00           N
ATOM      2  CA  HIS A   1      50.197  25.578  10.784  1.00 16.00           C
ATOM      3  C   HIS A   1      49.169  26.701  10.917  1.00 16.00           C
ATOM      4  O   HIS A   1      48.241  26.524  11.749  1.00 16.00           O
ATOM      5  CB  HIS A   1      51.312  26.048   9.843  1.00 16.00           C
ATOM      6  CG  HIS A   1      50.958  26.068   8.340  1.00 16.00           C
ATOM      7  ND1 HIS A   1      49.636  26.144   7.860  1.00 16.00           N
ATOM      8  CD2 HIS A   1      51.797  26.043   7.286  1.00 16.00           C
ATOM      9  CE1 HIS A   1      49.691  26.152   6.454  1.00 17.00           C
ATOM     10  NE2 HIS A   1      51.046  26.090   6.098  1.00 17.00           N
ATOM     11  N   SER A   2      49.788  27.850  10.784  1.00 16.00           N
ATOM     12  CA  SER A   2      49.138  29.147  10.620  1.00 15.00           C
ATOM     13  C   SER A   2      47.713  29.006  10.110  1.00 15.00           C
ATOM     14  O   SER A   2      46.740  29.251  10.864  1.00 15.00           O
ATOM     15  CB  SER A   2      49.875  29.930   9.569  1.00 16.00           C
ATOM     16  OG  SER A   2      49.145  31.057   9.176  1.00 19.00           O
ATOM     17  N   GLN A   3      47.620  28.367   8.973  1.00 15.00           N
ATOM     18  CA  GLN A   3      46.287  28.193   8.308  1.00 14.00           C
ATOM     19  C   GLN A   3      45.406  27.172   8.963  1.00 14.00           C

Notice that each line or record begins with the record type ATOM. The atom serial number is the next item in each record.

The atom name is the third item in the record. Notice that the first one or two characters of the atom name consists of the chemical symbol for the atom type. All the atom names beginning with C are carbon atoms; N indicates a nitrogen and O indicates oxygen. In amino acid residues, the next character is the remoteness indicator code, which is transliterated according to:

αA
βB
γG
δD
εE
ζZ
ηH
The next character of the atom name is a branch indicator, if required.

The next data field is the residue type. Notice that each record contains the residue type. In this example, the first residue in the chain is HIS (histidine) and the second residue is a SER (serine).

The next data field contains the chain identifier, in this case A.

The next data field contains the residue sequence number. Notice that as the residue changes from histidine to serine, the residue number changes from 1 to 2. Two like residues may be adjacent to one another, so the residue number is important for distinguishing between them.

The next three data fields contain the X, Y, and Z coordinate values, respectively. The last three fields shown are the occupancy, temperature factor (B-factor), and element symbol.

The spacing of the data fields is crucial. If a data field does not apply, it should be left blank.

The glucagon data file continues in this manner until the final residue is reached:

ATOM    239  N   THR A  29       3.391  19.940  12.762  1.00 21.00           N
ATOM    240  CA  THR A  29       2.014  19.761  13.283  1.00 21.00           C
ATOM    241  C   THR A  29       0.826  19.943  12.332  1.00 23.00           C
ATOM    242  O   THR A  29       0.932  19.600  11.133  1.00 30.00           O
ATOM    243  CB  THR A  29       1.845  20.667  14.505  1.00 21.00           C
ATOM    244  OG1 THR A  29       1.214  21.893  14.153  1.00 21.00           O
ATOM    245  CG2 THR A  29       3.180  20.968  15.185  1.00 21.00           C
ATOM    246  OXT THR A  29      -0.317  20.109  12.824  1.00 25.00           O
TER     247      THR A  29
Note that this residue includes the extra oxygen atom OXT on the terminal carboxyl group. Other than OXT and the rarely seen HXT, atoms in standard nucleotides and amino acids in version 3.0 PDB files are named according to the IUPAC recommendations (Markley et al., Pure Appl Chem 70:117 (1998)). The TER record terminates the amino acid chain.

A more complicated protein, hemoglobin, consists of four amino acid chains, each with an associated heme group. There are two alpha chains (identifiers A and C) and two beta chains (identifiers B and D). The first ten lines of coordinates for this molecule (entry 3hhb) are:

ATOM      1  N   VAL A   1       6.452  16.459   4.843  7.00 47.38           N
ATOM      2  CA  VAL A   1       7.060  17.792   4.760  6.00 48.47           C
ATOM      3  C   VAL A   1       8.561  17.703   5.038  6.00 37.13           C
ATOM      4  O   VAL A   1       8.992  17.182   6.072  8.00 36.25           O
ATOM      5  CB  VAL A   1       6.342  18.738   5.727  6.00 55.13           C
ATOM      6  CG1 VAL A   1       7.114  20.033   5.993  6.00 54.30           C
ATOM      7  CG2 VAL A   1       4.924  19.032   5.232  6.00 64.75           C
ATOM      8  N   LEU A   2       9.333  18.209   4.095  7.00 30.18           N
ATOM      9  CA  LEU A   2      10.785  18.159   4.237  6.00 35.60           C
ATOM     10  C   LEU A   2      11.247  19.305   5.133  6.00 35.47           C
At the end of chain A, the heme group records appear:
ATOM   1058  N   ARG A 141      -6.466  12.036 -10.348  7.00 19.11           N
ATOM   1059  CA  ARG A 141      -7.922  12.248 -10.253  6.00 26.80           C
ATOM   1060  C   ARG A 141      -8.119  13.499  -9.393  6.00 28.93           C
ATOM   1061  O   ARG A 141      -7.112  13.967  -8.853  8.00 28.68           O
ATOM   1062  CB  ARG A 141      -8.639  11.005  -9.687  6.00 24.11           C
ATOM   1063  CG  ARG A 141      -8.153  10.551  -8.308  6.00 19.20           C
ATOM   1064  CD  ARG A 141      -8.914   9.319  -7.796  6.00 21.53           C
ATOM   1065  NE  ARG A 141      -8.517   9.076  -6.403  7.00 20.93           N
ATOM   1066  CZ  ARG A 141      -9.142   8.234  -5.593  6.00 23.56           C
ATOM   1067  NH1 ARG A 141     -10.150   7.487  -6.019  7.00 19.04           N
ATOM   1068  NH2 ARG A 141      -8.725   8.129  -4.343  7.00 25.11           N
ATOM   1069  OXT ARG A 141      -9.233  14.024  -9.296  8.00 40.35           O
TER    1070      ARG A 141
HETATM 1071 FE   HEM A   1       8.128   7.371 -15.022 24.00 16.74          FE
HETATM 1072  CHA HEM A   1       8.617   7.879 -18.361  6.00 17.74           C
HETATM 1073  CHB HEM A   1      10.356  10.005 -14.319  6.00 18.92           C
HETATM 1074  CHC HEM A   1       8.307   6.456 -11.669  6.00 11.00           C
HETATM 1075  CHD HEM A   1       6.928   4.145 -15.725  6.00 13.25           C
The last residue in the alpha chain is an ARG (arginine). Again, the extra oxygen atom OXT appears in the terminal carboxyl group. The TER record indicates the end of the peptide chain. It is important to have TER records at the end of peptide chains so a bond is not drawn from the end of one chain to the start of another.

In the example above, the TER record is correct and should be present, but the molecule chain would still be terminated at that point even without a TER record, because HETATM residues are not connected to other residues or to each other. The heme group is a single residue made up of HETATM records.

After the heme group associated with chain A, chain B begins:

HETATM 1109  CAD HEM A   1       7.618   5.696 -20.432  6.00 21.38           C
HETATM 1110  CBD HEM A   1       8.947   5.143 -20.947  6.00 29.03           C
HETATM 1111  CGD HEM A   1       9.047   5.155 -22.461  6.00 30.08           C
HETATM 1112  O1D HEM A   1      10.139   5.458 -22.959  8.00 33.72           O
HETATM 1113  O2D HEM A   1       8.096   4.833 -23.177  8.00 33.55           O
ATOM   1114  N   VAL B   1       9.143 -20.582   1.231  7.00 48.92           N
ATOM   1115  CA  VAL B   1       8.824 -20.084  -0.109  6.00 52.26           C
ATOM   1116  C   VAL B   1       9.440 -20.964  -1.190  6.00 57.72           C
ATOM   1117  O   VAL B   1       9.768 -22.138  -0.985  8.00 55.05           O
ATOM   1118  CB  VAL B   1       9.314 -18.642  -0.302  6.00 58.48           C
ATOM   1119  CG1 VAL B   1       8.269 -17.606   0.113  6.00 59.43           C
ATOM   1120  CG2 VAL B   1      10.683 -18.373   0.331  6.00 45.96           C

Here the TER card is implicit in the start of a new chain.

Protein Data Bank format relies on the concept of residues:

Common Errors in PDB Format Files

If a data file fails to display correctly, it is sometimes difficult to determine where in the hundreds of lines of data the mistake occurred. This section enumerates some of the most common errors found in PDB files.

Program-Generated PDB Files

Spurious Long Bonds

A couple of common errors in program-generated PDB files result in the display of very long bonds between residues:

Apart from any format errors, Chimera also uses long bonds to indicate the underlying connectivity across chain segments that lack coordinates (e.g., regions of missing density due to crystallographic disorder). Regardless of their cause, long bonds in Chimera can be hidden with the command ~longbond.

Misaligned Atom Names

Incorrectly aligned atom names in PDB records can cause problems. Atom names are composed of an atomic (element) symbol right-justified in columns 13-14, and trailing identifying characters left-justified in columns 15-16. A single-character element symbol should not appear in column 13 unless the atom name has four characters (for example, see Hydrogen Atoms). Many programs simply left-justify all atom names starting in column 13. The difference can be seen clearly in a short segment of hemoglobin (entry 3hhb):

Correct:
HETATM 1071 FE   HEM A   1       8.128   7.371 -15.022 24.00 16.74          FE
HETATM 1072  CHA HEM A   1       8.617   7.879 -18.361  6.00 17.74           C
HETATM 1073  CHB HEM A   1      10.356  10.005 -14.319  6.00 18.92           C
HETATM 1074  CHC HEM A   1       8.307   6.456 -11.669  6.00 11.00           C
HETATM 1075  CHD HEM A   1       6.928   4.145 -15.725  6.00 13.25           C
Incorrect:
HETATM 1071 FE   HEM A   1       8.128   7.371 -15.022 24.00 16.74          FE
HETATM 1072 CHA  HEM A   1       8.617   7.879 -18.361  6.00 17.74           C
HETATM 1073 CHB  HEM A   1      10.356  10.005 -14.319  6.00 18.92           C
HETATM 1074 CHC  HEM A   1       8.307   6.456 -11.669  6.00 11.00           C
HETATM 1075 CHD  HEM A   1       6.928   4.145 -15.725  6.00 13.25           C

Hand-Edited PDB Files

Duplicate Atom Names

One possible editing mistake is the failure to uniquely name all atoms within a given residue. In the following example, two atoms in the same residue are named CA:

ATOM    185  N   VAL A  23      13.455  17.883  10.517  1.00  7.00           N
ATOM    186  CA  VAL A  23      12.574  17.403  11.589  1.00  7.00           C
ATOM    187  C   VAL A  23      11.283  18.205  11.729  1.00  7.00           C
ATOM    188  O   VAL A  23      10.233  17.600  12.052  1.00  7.00           O
ATOM    189  CA  VAL A  23      13.339  17.278  12.906  1.00 10.00           C
ATOM    190  CG1 VAL A  23      12.441  17.004  14.108  1.00 13.00           C
ATOM    191  CG2 VAL A  23      14.455  16.248  12.794  1.00 13.00           C
ATOM    192  N   GLN A  24      11.255  19.253  10.941  1.00  8.00           N
ATOM    193  CA  GLN A  24      10.082  20.114  10.818  1.00  8.00           C
ATOM    194  C   GLN A  24       9.158  19.638   9.692  1.00  8.00           C
Depending on the display program, the residue may be shown with incorrect connectivity, or it may become evident only upon labeling that the residue is missing a CB atom.

Residues Out of Sequence

In the following example, the second residue in the file is erroneously numbered residue 5. Many display programs will show this residue as connected to residues 1 and 3. If this residue was meant to be connected to residues 4 and 6 instead, it should appear between those residues in the PDB file.

ATOM      1  N   HIS A   1      49.668  24.248  10.436  1.00 25.00           N
ATOM      2  CA  HIS A   1      50.197  25.578  10.784  1.00 16.00           C
ATOM      3  C   HIS A   1      49.169  26.701  10.917  1.00 16.00           C
ATOM      4  O   HIS A   1      48.241  26.524  11.749  1.00 16.00           O
ATOM      5  CB  HIS A   1      51.312  26.048   9.843  1.00 16.00           C
ATOM      6  CG  HIS A   1      50.958  26.068   8.340  1.00 16.00           C
ATOM      7  ND1 HIS A   1      49.636  26.144   7.860  1.00 16.00           N
ATOM      8  CD2 HIS A   1      51.797  26.043   7.286  1.00 16.00           C
ATOM      9  CE1 HIS A   1      49.691  26.152   6.454  1.00 17.00           C
ATOM     10  NE2 HIS A   1      51.046  26.090   6.098  1.00 17.00           N
ATOM     11  N   SER A   5      49.788  27.850  10.784  1.00 16.00           N
ATOM     12  CA  SER A   5      49.138  29.147  10.620  1.00 15.00           C
ATOM     13  C   SER A   5      47.713  29.006  10.110  1.00 15.00           C
ATOM     14  O   SER A   5      46.740  29.251  10.864  1.00 15.00           O
ATOM     15  CB  SER A   5      49.875  29.930   9.569  1.00 16.00           C
ATOM     16  OG  SER A   5      49.145  31.057   9.176  1.00 19.00           O
ATOM     17  N   GLN A   3      47.620  28.367   8.973  1.00 15.00           N
ATOM     18  CA  GLN A   3      46.287  28.193   8.308  1.00 14.00           C

Common Typos

Sometimes the letter l is accidentally substituted for the number 1. This has different repercussions depending on where in the file the error occurs; a grossly misplaced atom may indicate the presence of such an error in a coordinate field. These errors can be located readily if the text of the data file appears in uppercase, by invoking a text editor to search for all instances of the lowercase letter l.

Hydrogen Atoms

In brief, conventions for hydrogen atoms in version 3.0 PDB format are as follows:

In the following excerpt from entry 1vm3, atom H is attached to atom N. Atom HA is attached to atom CA; the remoteness indicator A is the same for these atoms. Two hydrogen atoms are connected to CB, one is connected to CG, three are connected to CD1, and three are connected to CD2.

ATOM     10  N   LEU A   2       4.595   6.365   3.756  1.00  0.00           N
ATOM     11  CA  LEU A   2       4.471   5.443   2.633  1.00  0.00           C
ATOM     12  C   LEU A   2       5.841   5.176   2.015  1.00  0.00           C
ATOM     13  O   LEU A   2       6.205   4.029   1.755  1.00  0.00           O
ATOM     14  CB  LEU A   2       3.526   6.037   1.578  1.00  0.00           C
ATOM     15  CG  LEU A   2       2.790   4.919   0.823  1.00  0.00           C
ATOM     16  CD1 LEU A   2       3.803   3.916   0.262  1.00  0.00           C
ATOM     17  CD2 LEU A   2       1.817   4.196   1.769  1.00  0.00           C
ATOM     18  H   LEU A   2       4.169   7.246   3.704  1.00  0.00           H
ATOM     19  HA  LEU A   2       4.063   4.514   2.992  1.00  0.00           H
ATOM     20  HB2 LEU A   2       2.804   6.675   2.065  1.00  0.00           H
ATOM     21  HB3 LEU A   2       4.099   6.623   0.873  1.00  0.00           H
ATOM     22  HG  LEU A   2       2.234   5.353   0.004  1.00  0.00           H
ATOM     23 HD11 LEU A   2       4.648   4.447  -0.148  1.00  0.00           H
ATOM     24 HD12 LEU A   2       3.334   3.331  -0.516  1.00  0.00           H
ATOM     25 HD13 LEU A   2       4.137   3.260   1.052  1.00  0.00           H
ATOM     26 HD21 LEU A   2       0.941   3.892   1.216  1.00  0.00           H
ATOM     27 HD22 LEU A   2       1.522   4.860   2.568  1.00  0.00           H
ATOM     28 HD23 LEU A   2       2.296   3.323   2.188  1.00  0.00           H

PQR Variant of PDB Format

Several programs use a modified PDB format called PQR, in which atomic partial charge (Q) and radius (R) fields follow the X,Y,Z coordinate fields in ATOM and HETATM records. An excerpt:

ATOM      1  N   ALA     1      46.457  12.189  21.556  0.1414 1.8240
ATOM      2  CA  ALA     1      47.614  11.997  22.448  0.0962 1.9080
ATOM      3  C   ALA     1      47.538  12.947  23.645  0.6163 1.9080
ATOM      4  O   ALA     1      46.441  13.476  23.962 -0.5722 1.6612
ATOM      5  CB  ALA     1      48.911  12.134  21.650 -0.0597 1.9080
ATOM      6  H2  ALA     1      45.672  11.684  21.917  0.1997 0.6000
ATOM      7  H3  ALA     1      46.235  13.163  21.506  0.1997 0.6000
ATOM      8  H   ALA     1      46.683  11.849  20.642  0.1997 0.6000
ATOM      9  HA  ALA     1      47.603  11.052  22.786  0.0889 1.1000
ATOM     10  HB1 ALA     1      49.041  11.319  21.087  0.0300 1.4870
ATOM     11  HB3 ALA     1      48.855  12.941  21.064  0.0300 1.4870
ATOM     12  HB2 ALA     1      49.679  12.231  22.281  0.0300 1.4870
ATOM     13  N   ASP     2      48.702  13.128  24.279 -0.5163 1.8240
ATOM     14  CA  ASP     2      48.826  13.956  25.493  0.0381 1.9080
ATOM     15  C   ASP     2      48.614  15.471  25.323  0.5366 1.9080
ATOM     16  O   ASP     2      49.292  16.362  24.807 -0.5819 1.6612
ATOM     17  CB  ASP     2      50.156  13.635  26.226 -0.0303 1.9080
ATOM     18  CG  ASP     2      49.984  12.419  27.136  0.7994 1.9080
ATOM     19  OD1 ASP     2      50.595  12.308  28.221 -0.8014 1.6612
ATOM     20  OD2 ASP     2      49.198  11.502  26.778 -0.8014 1.6612
ATOM     21  H   ASP     2      49.511  12.637  23.845  0.2936 0.6000
ATOM     22  HA  ASP     2      48.104  13.630  26.146  0.0880 1.3870
ATOM     23  HB3 ASP     2      50.392  14.413  26.773 -0.0122 1.4870
ATOM     24  HB2 ASP     2      50.832  13.431  25.545 -0.0122 1.4870
PQR format is rather loosely defined and varies according to which program is producing or using the file. For example, APBS requires only that all fields be whitespace-delimited.

If an ATOM or HETATM record being read by Chimera is not in PDB format, Chimera next tries to read it as PQR format. In that case, all fields up to and including the coordinates are still expected to adhere to the standard format, but the next two eight-column fields are each expected to contain a floating-point number: charge is read from columns 55-62 and radius is read from columns 63-70. The values are assigned as the atom attributes charge and radius, respectively.

PDB2PQR is a program for structure cleanup, charge/radius assignment, and PQR file generation. See also the PDB2PQR tool in Chimera.


UCSF Computer Graphics Laboratory / May 2020