Pdb file coordinates units

First, you may color each chain differently to show the packing of different chains in the molecule as shown in the bottom image. Then, you can color each chain using a rainbow of colors from one end of the chain to the other to highlight its folding characteristics as shown at the top. Both of these methods are available in most molecular graphics programs. The molecule shown here is hemolysin from PDB structure 7ahl. If we were able to hold an atom rigidly fixed in one place, we could observe its distribution of electrons in an ideal situation.

The image would be dense towards the center with the density falling off further from the nucleus. When you look at experimental electron density distributions, however, the electrons usually have a wider distribution than this ideal. This may be due to vibration of the atoms, or differences between the many different molecules in the crystal lattice.

The observed electron density will include an average of all these small motions, yielding a slightly smeared image of the molecule. These motions, and the resultant smearing of the electron density, are incorporated into the atomic model by a B-value or temperature factor.

The amount of smearing is proportional to the magnitude of the B-value. Values under 10 create a model of the atom that is very sharp, indicating that the atom is not moving much and is in the same position in all of the molecules in the crystal. Values greater than 50 or so indicate that the atom is moving so much that it can barely been seen.

This is often the case for atoms at the surface of proteins, where long side chains are free to wag in the surrounding water.

Again from entry 4hhb:. The example shown is from a myoglobin structure solved at 2. Two histidine amino acids are shown. On the left is HIS93, which coordinates with the iron atom and thus, is held firmly in place. It has B-values in the range of notice how the contours nicely surround the whole amino acid, revealing a sharp electron density.

On the right is HIS81, which is exposed on the surface of the protein and has higher B-values in the range of Also note how the contours enclose a smaller space, showing a smaller region with high electron density for this amino acid because the overall electron density is weakly smeared in the space around the contours. The picture shows the whole molecule, with the atoms colored by the temperature factors.

For any given entry, the default view on the Structure Summary page shows the biological assembly. The forward and backward arrows at the top of the visualization box allow toggling between the asymmetric unit and biological assembly images.

In the case that there are multiple biological assemblies for the entry, the forward arrow can be used to browse through all of them. The biological assembly files can be downloaded from the "Download Files" menu options on the top right corner. For an example see entry 2bfu. Krissinel and K. Henrick Inference of macromolecular assemblies from crystalline state. Lawson, S. Dutta, J. Westbrook, K. Henrick, H. Berman Representation of viruses in the remediated PDB archive.

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Toggle navigation PDB Educational portal of. Biological Assemblies. Dealing with Coordinates. Methods for Determining Structure. Missing Coordinates and Biological Assemblies. Molecular Graphics Programs. 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. In brief, conventions for hydrogen atoms in version 3. A hydrogen atom name starts with H.

The next part of the name is based on the name of the connected nonhydrogen atom. For example, in amino acid residues, H is followed by the remoteness indicator if any of the connected atom, followed by the branch indicator if any of the connected atom; if more than one hydrogen is connected to the same atom, an additional digit is appended so that each hydrogen atom will have a unique name. If the name of a hydrogen has four characters, it is left-justified starting in column 13; if it has fewer than four characters, it is left-justified starting in column In the following excerpt from entry 1vm3 , atom H is attached to atom N.

For example, APBS requires only that all fields be whitespace-delimited. 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 and radius is read from columns The values are assigned as the atom attributes charge and radius , respectively.

Nonstandard residues include inhibitors, cofactors, ions, and solvent. 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. One record per helix. The x,y,z coordinates are followed by a number, which is 1 in most cases. This is called occupancy. Sometimes the side chain of an amino acid may have two or more different conformations due to local flexibility.

These conformations can be distinguished in the electron density map of the structure. In this case the crystallographer will build all conformations and for each atom refine a parameter called occupancy 1 for full occupancy, The numbers in the last column in the file are called the temperature factors, or B-factor, for each atom in the structure.

The B-factor describes the displacement of the atomic positions from an average mean value mean-square displacement. Higher flexibility results in larger displacements, and eventually lower electron density. This is simply because the atoms of a flexible side chain or other part of the structure will be distributed over a larger volume, leading to lower density per unit of volume. In many graphics programs we can color a protein chain according to B-factor values.

Areas with high B-factors are usually colored red hot , while low B-factors are colored blue cold. An inspection of a PDB structure with such coloring scheme will immediately reveal regions with high flexibility.