Protein Data Bank: Difference between revisions

Line 17:

Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and removes some errors. Remediation involves changes in the PDB data format. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB].

Here are some examples of changes that occurred in remediations affecting the PDB format. Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].)

Here are some examples of changes that occurred in remediations affecting the PDB format. Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Chime]] unable to deal with the remediated nucleic acids.

In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]

Obsolete (unremediated) versions of the data files were saved and may be obtained; see [[Getting Unremediated PDB Files]].

Protein Data Bank: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 17: / Line 17: @@
 Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and removes some errors. Remediation involves changes in the PDB data format. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB].
-Here are some examples of changes that occurred in remediations affecting the PDB format. Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].)
+Here are some examples of changes that occurred in remediations affecting the PDB format. Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Chime]] unable to deal with the remediated nucleic acids.
+In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]
 Obsolete (unremediated) versions of the data files were saved and may be obtained; see [[Getting Unremediated PDB Files]].