Protein data bank file reader

If ModelNumValue does not correspond to an existing mode number in File , then pdbread reads the coordinate information of all the models. The Sequence field is also a structure containing sequence information in the following subfields:. ResidueNames — Contains the three-letter codes for the sequence residues.

Sequence — Contains the single-letter codes for the sequence residues. If the sequence has modified residues, then the ResidueNames subfield might not correspond to the standard three-letter amino acid codes.

In this case, the Sequence subfield will contain the modified residue code in the position corresponding to the modified residue. The modified residue code is provided in the ModifiedResidues field. The Model field is also a structure or an array of structures containing coordinate information. That's a tentative change, and needs to be tested. We can reword the conditionals. I'm leaving two append blocks because I think it makes the logic clearer. Reworking the conditions so there is only one append statement will not improve speed.

So an alternative design is to read the whole file as an appropriate structured array, and then filter out the desired elements. A function like this should do it. I haven't tested it, so I'm sure there are some bugs. I think speed will be similar, unless you are skipping a large number of lines.

Both approaches have to read all lines, and that is the main time consumer. Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group.

There are two alpha chains identifiers A and C and two beta chains identifiers B and D. 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.

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. Apart from any format errors, Chimera also uses long bonds to indicate the underlying connectivity across chain segments that lack coordinates e.

Incorrectly aligned atom names in PDB records can cause problems. Atom names are composed of an atomic element symbol right -justified in columns , and trailing identifying characters left -justified in columns 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 The difference can be seen clearly in a short segment of hemoglobin entry 3hhb :.

One possible editing mistake is the failure to uniquely name all atoms within a given residue. 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. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.

The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks black vertical boxes are calculated with respect to all X-ray structures available prior to Resolution-specific percentile ranks white vertical boxes are calculated considering entries with similar resolution. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts.

EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches. Each node on the graph is a publication, and nodes are linked when they share MeSH terms. Go to the Downloads Page. Go to the Sequences Downloads Page.

Downloads are provided for: Coordinates of first chemical component instance from each PDB entry Coordinates of all chemical component instances from each PDB entry Ideal coordinates from Chemical Component Dictionary. Go to the Ligands Downloads Page. PDB is an online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

View iconic illustrations by the gifted artist Irving Geis in context with PDB structures and educational information. Read about the Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. Use the new Group option to simplify results based on sequence identity, UniProt ID, and group depositions.

Deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to EMDB will become mandatory starting February 25, The inaugural PDB50 symposium hosted by ASBMB hosted speakers from around the world who have made tremendous advances in structural biology and bioinformatics.