Protein Data Bank FilesStructures of proteins and nucleic acids are available in PDB files.1 These structures are derived from physical studies of molecules (for example, x-ray diffraction or nuclear magnetic resonance (NMR) analyses). HyperChem can interpret and display structures stored in all PDB files that contain atomic coordinates, and can also store new molecular structures in PDB-type files. Obtaining PDB FilesThe HyperChem distribution disks contain several sample PDB files. You can obtain the complete PDB collection, containing about 17000 structures, from the Research Collaboratory for Structural Bioinformatics (RCSB). Alternatively, you can download a specific PDB file. For information, contact: Reading PDB FilesHyperChem can read all PDB files that contain atomic coordinates, up to the limit of the computer memory. HyperChem uses the PDB information on atomic coordinates, plus the information in its own TPL files (see ), to reconstruct standard amino acid and nucleic acid residues. For HETATM records and atoms that are not included in TPL files, HyperChem uses atomic coordinates and CONECT records from the PDB file to reconstruct a molecular system. HyperChem expects that PDB files will follow the formatting standards described by the maintainers of the PDB archive. Some software creates "PDB" files that do not follow this format properly; for example, the data entries on a line of the file may be in the wrong columns, or shifted left or right within a section. If you use the script command " non-standard-pdb-names = yes ", HyperChem will attempt to make allowances for incorrect formatting. Use of this command may prevent correct reading of files which do conform to the standards. Most PDB files contain all the information that is necessary for HyperChem to regenerate the structure. However, if a PDB file includes non-standard residues which are not in HyperChem's template files, but does not include information about bonding and/or hydrogen atoms, then HyperChem will not be able to process the structure properly. If the file does not have bonding information, you will probably end up with a number of disconnected atoms in the workspace which you will have to connect to form molecules. (See .) If the file does not include hydrogen atoms, you can add them with Build/Add Hydrogens .
Creating PDB-type FilesYou can save any molecular system in the workspace as a PDB-type file. Choose Save As on the File menu and L-click on PDB in the Save File dialog box. HyperChem provides the filename extension .ent , but you have to enter a new filename in the File Name text box. The PDB file can contain 13 types of records (each record has a title and takes up one line in the file): HEADER These are all comment records from a PDB file that you can enter or edit in the Save File dialog box.
ATOMThe identity and coordinates of each heavy atom in the molecular system. These atoms must be part of the standard set of residues that HyperChem recognizes (see and ). HETATMThe identity and coordinates of all heavy atoms that are not part of standard residues. Standard residues belong to the set that HyperChem recognizes (see and ). CONECTThe numbers of atoms directly bonded to each other. These numbers come from the ATOM or HETATM records. The Numbers label ( Choose Labels on the Display menu) also uses these numbers. CONECT records appear for HETATMs and for all atoms if you choose the Connectivity option (see below). 1. The Protein Data Bank is operated by the Research Collaboratory for Structural Bioinformatics (RCSB) and is supported by funds from the National Science Foundation, the Department of Energy, and two units of the National Institutes of Health: the National Institute of General Medical Sciences and the National Library of Medicine.
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