ATOM Records

Table 2-8. Format of the ATOM record. Co/wwnj Definition...

The data for non-reactively scattered Y atoms recorded at m/e 89 (not shown) exhibit typical features for impulsive inelastic scattering without appreciable long-lived complex formation.124,127 In the CM reference frame,... 

ProSa reads all it needs to know about a protein from a file in PDB format. A detailed description of this standard format is given at the RCSB website [2]. Of all record types within a PDB file, only the ATOM records are used by ProSa. They contain both the amino acid sequence of a certain protein chain and the atomic coordinates (example PDB files come with the ProSa distribution). If a PDB file contains more than one chain, only one is read. The first chain is read by default, other chains can be specified by providing the respective chain identifier. All molecules other than polypeptides are ignored. For energy calculations, ProSa takes into account C° and atoms. Care has to be taken when dealing with residue... 

An issue that has already been mentioned in section 11.2 is residue numbering. Residues listed in the ATOM records of a PDB file are not necessarily numbered consecutively, may not start with residue number 1, may have an additional insertion code, and may even be negative (see [2] for details). ProSa, in contrast, uses a sequential index to address residues the first residue gets number 1, the second residue number 2, and so on. In addition, some of the residues present in a PDB file may be skipped by ProSa, for example, because they are not a standard amino acid. As a consequence, you have to make sure that the residue(s) you substitute with mutate sequence or randomise sequence really correspond to those you have in focus. One hint is the correct wild-type amino acid, as displayed in the object name of the mutant. To get a list of PDB residue numbers of a certain object and how they are mapped to the sequential index, use print residue mapping object. ... 

ATOM records are used to specify molecules which occur frequently in biological systems. These are called the known molecules and include amino acids, heme, cofactors, some of the unnatural amino acids used by medicinal chemists and a variety of molecules of general interest to GRID users. Here is a Protein Data Bank ATOM record ... 

The PDB nomenclature uses the first six characters on a line in order to define different kinds of record, and this is an ATOM record. 

The sequence of ATOM records in a molecule is specified by PDB format. However HETATM records can be listed in any sequence, and the nitrogen has been moved to the 25th row of the new HETATM file. There is nothing special about its new position, and the user could just as easily have moved it to the first or last row of the file, or left it where it was. 

In a molecular structure file, an atom record typically contains all of the information about that atom the atomic number or symbol, the charge, coordinates, etc. When such a file is parsed into a SMILES string and an array of coordinates, it is important to be able to associate the proper coordinate with the proper atom. The use of canonical SMILES ensures this. Because canonical SMILES defines a unique order of the atoms in a molecule, that order is used to store the coordinates. Later sections of this chapter will discuss ways in which atomic coordinates might be stored in columns of a table. 

Fig. 2.7. Very high Rydberg states of the Ba atom recorded by laser spectroscopy using thermionic diode detection (after J.-P. Connerade et at. [27]).

Fig. 9.39. ATI spectrum for Ar atoms recorded for 616 nm (2eV) pulses with a pulse length of 0.2ps [9.241]...

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