PDB identification code - Revision history

Eric Martz: /* Future Plans for Expanded PDB Codes */

2024-04-08T19:06:45Z

Future Plans for Expanded PDB Codes

← Older revision		Revision as of 19:06, 8 April 2024
Line 39:		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		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		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===		===Versioning===

Eric Martz: /* Limited Number of 4-Character PDB Codes */

2024-04-08T17:54:31Z

Limited Number of 4-Character PDB Codes

← Older revision		Revision as of 17:54, 8 April 2024
Line 29:		Line 29:
	==Limited Number of 4-Character PDB Codes==		==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 Thus, the ~170,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up nearly half of the available codes.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==		==Future Plans for Expanded PDB Codes==

Eric Martz: /* Limited Number of 4-Character PDB Codes */

2024-04-08T17:53:38Z

Limited Number of 4-Character PDB Codes

← Older revision		Revision as of 17:53, 8 April 2024
Line 29:		Line 29:
	==Limited Number of 4-Character PDB Codes==		==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, 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.		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.

	==Future Plans for Expanded PDB Codes==		==Future Plans for Expanded PDB Codes==

Eric Martz: /* Limited Number of 4-Character PDB Codes */

2024-04-08T17:51:26Z

Limited Number of 4-Character PDB Codes

← Older revision		Revision as of 17:51, 8 April 2024
Line 29:		Line 29:
	==Limited Number of 4-Character PDB Codes==		==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. By approximately ~~2024~~, 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.		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, 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==		==Future Plans for Expanded PDB Codes==

Eric Martz: /* Versioning */

2021-04-21T20:34:28Z

Versioning

← Older revision		Revision as of 20:34, 21 April 2021
Line 55:		Line 55:
	</blockquote>		</blockquote>
	where "v1" designates a major version, and "-2" a minor version.<ref name="news1" /> "xyz" is a constant that signifies an atomic coordinate file. Other types of data files might use the same PDB accession codes in future.		where "v1" designates a major version, and "-2" a minor version.<ref name="news1" /> "xyz" is a constant that signifies an atomic coordinate file. Other types of data files might use the same PDB accession codes in future.

			==Document Object Identifiers (DOI) for PDB Entries==
			[http://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d Each PDB entry is accessible through a DOI]. For example, 6ef8 is accessible as [http://doi.org/10.2210/pdb6ef8/pdb doi.org/10.2210/pdb6ef8/pdb].

	==See Also==		==See Also==

Eric Martz: /* Limited Number of 4-Character PDB Codes */

2021-04-21T20:29:55Z

Limited Number of 4-Character PDB Codes

← Older revision		Revision as of 20:29, 21 April 2021
Line 29:		Line 29:
	==Limited Number of 4-Character PDB Codes==		==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 ~~~132~~,000 entries in mid 2017 (plus withdrawn and superceded entries) have used up ~~about one third~~ of the available codes. ~~Someday~~ 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.		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. By approximately 2024, 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==		==Future Plans for Expanded PDB Codes==

Eric Martz: /* See Also */

2021-01-19T19:12:01Z

Eric Martz: /* PDB codes have been permanently associated with a single structure */

2019-10-17T20:51:03Z

PDB codes have been permanently associated with a single structure

← Older revision		Revision as of 20:51, 17 October 2019
Line 25:		Line 25:
	Once a PDB code is assigned to a given structure, it's forever, even in those cases when a structure is withdrawn (retired from the database), like [[3luw]], or superceded by a newer or corrected structure, like [[1ace]]. If requesting a page for a superseded structure, like [[1aak]], Proteopedia will automatically display the newest structure [[2aak]]. Look for the explanation in the 'Structural Highlights' section of each page.		Once a PDB code is assigned to a given structure, it's forever, even in those cases when a structure is withdrawn (retired from the database), like [[3luw]], or superceded by a newer or corrected structure, like [[1ace]]. If requesting a page for a superseded structure, like [[1aak]], Proteopedia will automatically display the newest structure [[2aak]]. Look for the explanation in the 'Structural Highlights' section of each page.

	In May, 2017, the PDB announced plans for a versioning system. This ~~would allow~~ multiple versions of the same entry to keep a single PDB code. See [[#Future Plans for Expanded PDB Codes\|below]].		In May, 2017, the PDB announced plans for a versioning system. This went into effect in July, 2019<ref name="news2" />. It allows multiple versions of the same entry to keep a single PDB code. See [[#Future Plans for Expanded PDB Codes\|below]].

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

Eric Martz at 20:49, 17 October 2019

2019-10-17T20:49:43Z

← Older revision		Revision as of 20:49, 17 October 2019
Line 42:		Line 42:

	===Versioning===		===Versioning===
	Along with the expanded accession codes, a versioning system ~~will be~~ introduced<ref name="news1" />.		Along with the expanded accession codes, a versioning system was introduced in mid-2019<ref name="news1" /><ref name="news2">PDB News July 31, 2019: [https://www.rcsb.org/news?year=2019&article=5d3ef68aea7d0653b99c87fd Improve your previously released coordinates AND keep your original PDB ID with OneDep]</ref>.
	<blockquote>		<blockquote>
	At present, revised atomic coordinates for an existing released PDB		At present, revised atomic coordinates for an existing released PDB

Eric Martz: /* Future Plans for Expanded PDB Codes */

2019-10-17T20:45:10Z

Future Plans for Expanded PDB Codes

← Older revision		Revision as of 20:45, 17 October 2019
Line 41:		Line 41:
	to the current four-character style."<ref name="news1" />		to the current four-character style."<ref name="news1" />

			===Versioning===
	Along with the expanded accession codes, a versioning system will be introduced<ref name="news1" />.		Along with the expanded accession codes, a versioning system will be introduced<ref name="news1" />.
	<blockquote>		<blockquote>

← Older revision		Revision as of 19:12, 19 January 2021
Line 58:		Line 58:
	==See Also==		==See Also==
	* [[PDB file format]]		* [[PDB file format]]
			* [[User:Eric Martz/Entertaining PDB codes\|Entertaining PDB codes]]

	==References==		==References==
	<references />		<references />