Atomic coordinate file: Difference between revisions
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*[http://mmcif.rcsb.org/ Protein Data Bank's website on mmCIF] | *[http://mmcif.rcsb.org/ Protein Data Bank's website on mmCIF] | ||
==ASN.1 Data Format== | |||
The [http://www.ncbi.nlm.nih.gov/ US National Center for Biotechnology Information] (NCBI) maintains a macromolecular structure database (derived from the [[Protein Data Bank]]) that is integrated with their ''Entrez'' cross-database search system, and their other databases of sequences, medical literature, inheritance, taxonomy, etc. They have chosen to maintain their [[Atomic coordinate files|atomic coordinate files]] in the Abstract Syntax Notation One (ASN.1) data format. | |||
*[http://www.ncbi.nlm.nih.gov/Sitemap/Summary/asn1.html Introduction to ASN.1 at NCBI] | |||
==Bonds: Connectivity== | ==Bonds: Connectivity== | ||
Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The [http://www.wwpdb.org/documentation/format30/index.html PDB data format] requires that covalent bonds be specified between atoms that are not members of [[Standard Residues]] in protein or nucleic acid chains. These are specified in CONECT records. | Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The [http://www.wwpdb.org/documentation/format30/index.html PDB data format] requires that covalent bonds be specified between atoms that are not members of [[Standard Residues]] in protein or nucleic acid chains. These are specified in CONECT records. | ||
