MDAnalysis parses the following PDB records (see PDB coordinate section for details):
- CRYST1 for unit cell dimensions A,B,C, alpha,beta,gamma
- ATOM or HETATM for serial, name, resName, chainID, resSeq, x, y, z, occupancy, tempFactor, segID
- CONECT records for bonds
- HEADER (:attr:`Universe.trajectory.header`)
- TITLE (:attr:`Universe.trajectory.title`)
- COMPND (:attr:`Universe.trajectory.compound`)
- REMARK (:attr:`Universe.trajectory.remarks`)
All other lines are ignored. Multi-MODEL PDB files are read as trajectories with a default timestep of 1 ps :ref:`(pass in the dt argument to change this) <universe-kwargs>`. Currently, MDAnalysis cannot read multi-model PDB files written by VMD, as VMD uses the keyword "END" to separate models instead of "MODEL"/"ENDMDL" keywords.
Important
Previously, MDAnalysis did not read elements from a file. Now, if valid elements are provided, MDAnalysis will read them in and will not guess them from atom names.
MDAnalysis attempts to read segid attributes from the segID column. If this column does not contain information, segments are instead created from chainIDs. If chainIDs are also not present, then segids are set to the default 'SYSTEM' value.
MDAnalysis can write both single-frame PDBs and convert trajectories to multi-model PDBs. If the Universe is missing fields that are :ref:`required in a PDB file <pdb-spec>`, MDAnalysis provides default values and raises a warning. There are 2 exceptions to this:
chainIDs: if a Universe does not havechainIDs, MDAnalysis uses the first character of the segmentsegidinstead.elements: Elements are always guessed from the atom name.
These are the default values:
CRYST1 fields
- names: 'X'
- altLocs: ''
- resnames: 'UNK'
- icodes: ''
- segids: ''
- resids: 1
- occupancies: 1.0
- tempfactors: 0.0
| COLUMNS | DATA TYPE | FIELD | DEFINITION |
|---|---|---|---|
| 1 - 6 | Record name | "CRYST1" | |
| 7 - 15 | Real(9.3) | a | a (Angstroms). |
| 16 - 24 | Real(9.3) | b | b (Angstroms). |
| 25 - 33 | Real(9.3) | c | c (Angstroms). |
| 34 - 40 | Real(7.2) | alpha | alpha (degrees). |
| 41 - 47 | Real(7.2) | beta | beta (degrees). |
| 48 - 54 | Real(7.2) | gamma | gamma (degrees). |
| 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 - 21 | 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. |
| 67 - 76 | String | segID | (unofficial CHARMM extension ?) |
| 77 - 78 | LString(2) | element | Element symbol, right-justified. |
| 79 - 80 | LString(2) | charge | Charge on the atom. |