PDB identification code: Difference between revisions

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==Limited Number of 4-Character PDB Codes==

There are 419,904 possible 4-character PDB identification codes<ref>Ten numerals plus 26 letters = 36. The first character is 1-9. (9)(363) = 419,904.</ref>. This could be increased to 466,560 if the numeral "0" is allowed as the first character<ref>In April, 2013. according to Rachel Kramer Green of the RCSB in Rutgers, NJ, there were no plans to use PDB codes beginning with 0. However, in July, 2017, the WWPDB FAQ states "The four-letter PDB identifier currently consists of a number (0-9) followed by 3 letters or numbers.".</ref>. Thus, the ~170,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up nearly half of the available codes. After approximately 2027<ref name="spring2024">[https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/deposit.html#two Resources for Supporting the Extended PDB ID Format

There are 419,904 possible 4-character PDB identification codes<ref>Ten numerals plus 26 letters = 36. The first character is 1-9. (9)(363) = 419,904.</ref>. This could be increased to 466,560 if the numeral "0" is allowed as the first character<ref>In April, 2013. according to Rachel Kramer Green of the RCSB in Rutgers, NJ, there were no plans to use PDB codes beginning with 0. However, in July, 2017, the WWPDB FAQ states "The four-letter PDB identifier currently consists of a number (0-9) followed by 3 letters or numbers.".</ref>. Thus, the ~170,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up nearly half of the available codes. After approximately 2027<ref name="spring2024">[https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/deposit.html#two Resources for Supporting the Extended PDB ID Format (pdb_00001abc)], Spring 2024 Issue of the RCSB PDB Newsletter.</ref>, a scheme that can accommodate more entries will be required, requiring revision of macromolecular visualization and modeling software programs that obtain data online, all of which, of necessity, currently require 4-character PDB codes. See plans for an expanded system in the following section.

(pdb_00001abc)], Spring 2024 Issue of the RCSB PDB Newsletter.</ref>, a scheme that can accommodate more entries will be required, requiring revision of macromolecular visualization and modeling software programs that obtain data online, all of which, of necessity, currently require 4-character PDB codes. See plans for an expanded system in the following section.

==Future Plans for Expanded PDB Codes==

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In addition to increasing the number of possible accession codes from ~4 x 104 to >109, this will facilitate "text mining detection of PDB entries in the published literature"<ref name="news1" />. The PDB also promises "For as long as practicable, the

wwPDB will continue assigning PDB codes that can be truncated losslessly

to the current four-character style."<ref name="news1" />

to the current four-character style."<ref name="news1" /> When 4-character codes are exhausted, new entries will be available in [[Atomic_coordinate_file#mmCIF_Data_Format|mmCIF format]] only, since the legacy [[PDB format]] will not accommodate 12-character IDs.

In 2024, the [[wwPDB]] plans to make a beta 12-character ID archive available in 2026<ref name="spring2024" />. In 2024, the wwPDB estimates that the 4-character IDs will be consumed in 2029<ref name="spring2024" />.

===Versioning===

PDB identification code: Difference between revisions

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@@ Line 29: / Line 29: @@
 ==Limited Number of 4-Character PDB Codes==
-There are 419,904 possible 4-character PDB identification codes<ref>Ten numerals plus 26 letters = 36. The first character is 1-9. (9)(36<sup>3</sup>) = 419,904.</ref>. This could be increased to 466,560 if the numeral "0" is allowed as the first character<ref>In April, 2013. according to Rachel Kramer Green of the RCSB in Rutgers, NJ, there were no plans to use PDB codes beginning with 0. However, in July, 2017, the WWPDB FAQ states "The four-letter PDB identifier currently consists of a number (0-9) followed by 3 letters or numbers.".</ref>. Thus, the ~170,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up nearly half of the available codes. After approximately 2027<ref name="spring2024">[https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/deposit.html#two Resources for Supporting the Extended PDB ID Format
+There are 419,904 possible 4-character PDB identification codes<ref>Ten numerals plus 26 letters = 36. The first character is 1-9. (9)(36<sup>3</sup>) = 419,904.</ref>. This could be increased to 466,560 if the numeral "0" is allowed as the first character<ref>In April, 2013. according to Rachel Kramer Green of the RCSB in Rutgers, NJ, there were no plans to use PDB codes beginning with 0. However, in July, 2017, the WWPDB FAQ states "The four-letter PDB identifier currently consists of a number (0-9) followed by 3 letters or numbers.".</ref>. Thus, the ~170,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up nearly half of the available codes. After approximately 2027<ref name="spring2024">[https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/deposit.html#two Resources for Supporting the Extended PDB ID Format (pdb_00001abc)], Spring 2024 Issue of the RCSB PDB Newsletter.</ref>, a scheme that can accommodate more entries will be required, requiring revision of macromolecular visualization and modeling software programs that obtain data online, all of which, of necessity, currently require 4-character PDB codes. See plans for an expanded system in the following section.
-(pdb_00001abc)], Spring 2024 Issue of the RCSB PDB Newsletter.</ref>, a scheme that can accommodate more entries will be required, requiring revision of macromolecular visualization and modeling software programs that obtain data online, all of which, of necessity, currently require 4-character PDB codes. See plans for an expanded system in the following section.
 ==Future Plans for Expanded PDB Codes==
@@ Line 40: / Line 39: @@
 In addition to increasing the number of possible accession codes from ~4 x 10<sup>4</sup> to >10<sup>9</sup>, this will facilitate "text mining detection of PDB entries in the published literature"<ref name="news1" />. The PDB also promises "For as long as practicable, the
 wwPDB will continue assigning PDB codes that can be truncated losslessly
-to the current four-character style."<ref name="news1" />
+to the current four-character style."<ref name="news1" /> When 4-character codes are exhausted, new entries will be available in [[Atomic_coordinate_file#mmCIF_Data_Format|mmCIF format]] only, since the legacy [[PDB format]] will not accommodate 12-character IDs.
+In 2024, the [[wwPDB]] plans to make a beta 12-character ID archive available in 2026<ref name="spring2024" />. In 2024, the wwPDB estimates that the 4-character IDs will be consumed in 2029<ref name="spring2024" />.
 ===Versioning===