Getting Unremediated PDB Files - Revision history

Eric Martz: /* How to get the unremediated version? */

2019-12-19T17:18:21Z

How to get the unremediated version?

← Older revision		Revision as of 17:18, 19 December 2019
Line 27:		Line 27:

	To uncompress the downloaded files:		To uncompress the downloaded files:
			* First try simply double-clicking the compressed file. On Macs (in 2019) this decompresses them.
	* For uncompressing the 2007 files that are in .Z format:		* For uncompressing the 2007 files that are in .Z format:
	** Both .Z and .gz files can be uncompressed in Windows using [http://www.7-zip.org/ 7-Zip], which is freeware and open source.		** Both .Z and .gz files can be uncompressed in Windows using [http://www.7-zip.org/ 7-Zip], which is freeware and open source.

Eric Martz: /* How to get the unremediated version? */

2019-12-19T17:08:25Z

How to get the unremediated version?

← Older revision		Revision as of 17:08, 19 December 2019
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	==How to get the unremediated version?==		==How to get the unremediated version?==
	Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.		<!--Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.-->

	The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the ~~RCSB~~ Protein Data Bank] in the		The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the World Wide Protein Data Bank] in the
	directory 20090316.		directory 20090316.

Eric Martz: /* See Also */ adding content

2009-12-26T03:07:26Z

Eric Martz: polishing

2009-12-26T03:06:26Z

polishing

← Older revision		Revision as of 03:06, 26 December 2009
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	''Please, note that .gz files can be displayed in Proteopedia without being uncompressed, since Jmol can read gzipped files directly.''		''Please, note that .gz files can be displayed in Proteopedia without being uncompressed, since Jmol can read gzipped files directly.''

			==See Also==
	~~See also~~ [[Standard Residues]] ~~and~~ [[Non-Standard Residues]]		*[[PDB#Remediation\|Remediation]]
			*[[Standard Residues]]
			*[[Non-Standard Residues]]

Eric Martz: linked first occurrence of 'remediation'

2009-12-26T03:04:38Z

linked first occurrence of 'remediation'

← Older revision		Revision as of 03:04, 26 December 2009
Line 1:		Line 1:
	Periodically, the [[Protein Data Bank]] remediates [[PDB files]] in the worldwide archive that it maintains. Two rounds of remediation took place between 2007 and 2009, in order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank].		Periodically, the [[Protein Data Bank]] remediates [[PDB files]] in the worldwide archive that it maintains. Two rounds of [[PDB#Remediation\|remediation]] took place between 2007 and 2009, in order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank].

	The unremediated PDB archive from before March 17, 2009 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316.		The unremediated PDB archive from before March 17, 2009 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316.

Eric Martz: /* Proteopedia avoids remediation-related problems */ polishing

2009-12-24T23:01:14Z

Proteopedia avoids remediation-related problems: polishing

← Older revision		Revision as of 23:01, 24 December 2009
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	==Proteopedia avoids remediation-related problems==		==Proteopedia avoids remediation-related problems==

	Following the experience of the 2009 remediation, Proteopedia automatically saves the version of the PDB file for which each molecular scene is developed, along with the Jmol script for the scene. When a new scene is developed with the [[SAT\|Scene Authoring Tools]], the current version of the PDB file is used and saved. Thus, subsequent remediations cannot inadvertantly corrupt scenes developed on earlier versions of the PDB file. (The 2009 remediation changed the order of atoms in some PDB files, which broke a few scenes until Proteopedia was modified to save the PDB file along with the scene script.)		Following the experience of the 2009 remediation, Proteopedia automatically saves the version of the PDB file for which each molecular scene is developed, along with the Jmol script for the scene. When a new scene is developed with the [[SAT\|Scene Authoring Tools]], the current version of the PDB file is used and saved. Thus, subsequent remediations cannot inadvertantly corrupt scenes developed on earlier versions of the PDB file. (The 2009 remediation changed the order of atoms in some PDB files, which broke a few scenes until Proteopedia was modified to save the PDB file along with the scene script. These were repaired by obtaining the unremediated PDB files and using them for these scenes.)

	==Why would you need an unremediated version of a pdb file?==		==Why would you need an unremediated version of a pdb file?==

Eric Martz: changed headings from === to ==

2009-12-24T23:00:19Z

changed headings from === to ==

← Older revision		Revision as of 23:00, 24 December 2009
Line 7:		Line 7:
	If a PDB file was released after December 2, 2008, it is not available in unremediated form.		If a PDB file was released after December 2, 2008, it is not available in unremediated form.

			==Proteopedia avoids remediation-related problems==
	===Proteopedia avoids remediation-related problems===

	Following the experience of the 2009 remediation, Proteopedia automatically saves the version of the PDB file for which each molecular scene is developed, along with the Jmol script for the scene. When a new scene is developed with the [[SAT\|Scene Authoring Tools]], the current version of the PDB file is used and saved. Thus, subsequent remediations cannot inadvertantly corrupt scenes developed on earlier versions of the PDB file. (The 2009 remediation changed the order of atoms in some PDB files, which broke a few scenes until Proteopedia was modified to save the PDB file along with the scene script.)		Following the experience of the 2009 remediation, Proteopedia automatically saves the version of the PDB file for which each molecular scene is developed, along with the Jmol script for the scene. When a new scene is developed with the [[SAT\|Scene Authoring Tools]], the current version of the PDB file is used and saved. Thus, subsequent remediations cannot inadvertantly corrupt scenes developed on earlier versions of the PDB file. (The 2009 remediation changed the order of atoms in some PDB files, which broke a few scenes until Proteopedia was modified to save the PDB file along with the scene script.)

	===Why would you need an unremediated version of a pdb file?===		==Why would you need an unremediated version of a pdb file?==
	A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]] (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2009 round; released March 17th 2009) also mainly affected nucleic acid residues and atoms.		A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]] (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2009 round; released March 17th 2009) also mainly affected nucleic acid residues and atoms.

	===How to get the unremediated version?===		==How to get the unremediated version?==
	Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.		Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.

Eric Martz: /* Why would you need an unremediated version of a pdb file? */ updated obsolete paragraph about Proteopedia

2009-12-24T22:57:42Z

Why would you need an unremediated version of a pdb file?: updated obsolete paragraph about Proteopedia

← Older revision		Revision as of 22:57, 24 December 2009
Line 7:		Line 7:
	If a PDB file was released after December 2, 2008, it is not available in unremediated form.		If a PDB file was released after December 2, 2008, it is not available in unremediated form.


			===Proteopedia avoids remediation-related problems===

			Following the experience of the 2009 remediation, Proteopedia automatically saves the version of the PDB file for which each molecular scene is developed, along with the Jmol script for the scene. When a new scene is developed with the [[SAT\|Scene Authoring Tools]], the current version of the PDB file is used and saved. Thus, subsequent remediations cannot inadvertantly corrupt scenes developed on earlier versions of the PDB file. (The 2009 remediation changed the order of atoms in some PDB files, which broke a few scenes until Proteopedia was modified to save the PDB file along with the scene script.)

	===Why would you need an unremediated version of a pdb file?===		===Why would you need an unremediated version of a pdb file?===
	A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]] (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2009 round; released March 17th 2009) also mainly affected nucleic acid residues and atoms.		A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]] (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2009 round; released March 17th 2009) also mainly affected nucleic acid residues and atoms.

	Proteopedia also needs the unremediated files (pre-March 17th 2009). Proteopedia actually premiered between the two rounds of remediation and relied on the atom serial numbers for saving the scenes, yet contacts the PDB to get the current PDB file. Thus when the March 17th remediated version of the database was released with differing atom serial numbers, scenes involving nucleic acid using the newer files often no longer looked correct because some atom serial numbers now do not match. A global fix for this is currently being worked on according to Eran Hodis and Jaime Prilusky (see the gray banner at the top of the page for updates).

	===How to get the unremediated version?===		===How to get the unremediated version?===

Eric Martz: corrected year to 2009 (3 places) and added introductory sentence at top of page.

2009-12-24T22:50:31Z

corrected year to 2009 (3 places) and added introductory sentence at top of page.

← Older revision		Revision as of 22:50, 24 December 2009
Line 1:		Line 1:
	Two rounds of remediation ~~have now taken~~ place between 2007 and 2009 to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank].		Periodically, the [[Protein Data Bank]] remediates [[PDB files]] in the worldwide archive that it maintains. Two rounds of remediation took place between 2007 and 2009, in order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank].

			The unremediated PDB archive from before March 17, 2009 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316.
	The unremediated PDB archive from before March 17, ~~2008~~ is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316.

	The unremediated PDB archive from before August 1, 2007 is available, as detailed [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904 here].		The unremediated PDB archive from before August 1, 2007 is available, as detailed [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904 here].
Line 10:		Line 9:

	===Why would you need an unremediated version of a pdb file?===		===Why would you need an unremediated version of a pdb file?===
	A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, ~~CHIME~~-based Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (~~2008~~ round; released March 17th ~~2000~~) also mainly affected nucleic acid residues and atoms.~~<br>~~		A significant change made in the course of the first round (2007) of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files from before the 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]] (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2009 round; released March 17th 2009) also mainly affected nucleic acid residues and atoms.

	Proteopedia also needs the unremediated files (pre-March 17th 2009). Proteopedia actually premiered between the two rounds of remediation and relied on the atom serial numbers for saving the scenes, yet contacts the PDB to get the current PDB file. Thus when the March 17th remediated version of the database was released with differing atom serial numbers, scenes involving nucleic acid using the newer files often no longer looked correct because some atom serial numbers now do not match. A global fix for this is currently being worked on according to Eran Hodis and Jaime Prilusky (see the gray banner at the top of the page for updates).		Proteopedia also needs the unremediated files (pre-March 17th 2009). Proteopedia actually premiered between the two rounds of remediation and relied on the atom serial numbers for saving the scenes, yet contacts the PDB to get the current PDB file. Thus when the March 17th remediated version of the database was released with differing atom serial numbers, scenes involving nucleic acid using the newer files often no longer looked correct because some atom serial numbers now do not match. A global fix for this is currently being worked on according to Eran Hodis and Jaime Prilusky (see the gray banner at the top of the page for updates).

Angel Herraez: 7-zip as a possible uncompressor

2009-04-13T17:49:30Z

7-zip as a possible uncompressor

@@ Line 14: / Line 14: @@
 ===How to get the unremediated version?===
-Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.<br>
+Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.
-<p>
-The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20090316.<br>
+The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the
-</p>
+directory 20090316.
-<p>
-These files come back in a compressed form. The 2007 files are .Z compressed, while the 2009 files are .gz compressed.<br>
+These files come back in a compressed form. The 2007 files are .Z compressed, while the 2009 files are .gz compressed.
-</p>
-<p>
+Thus to get the two forms of 1d66:
-Thus to get the two forms of 1d66:<br>
+* For prior to 2007 remediation: <nowiki>ftp://snapshots.wwpdb.org/20070731/pub/pdb/data/structures/all/pdb/pdb1d66.ent.Z</nowiki>
 See also [[Standard Residues]] and [[Non-Standard Residues]]

← Older revision		Revision as of 03:07, 26 December 2009
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	==See Also==		==See Also==
			*[[Atomic coordinate files]]
			*[[PDB file format]]
	*[[PDB#Remediation\|Remediation]]		*[[PDB#Remediation\|Remediation]]
	*[[Standard Residues]]		*[[Standard Residues]]
	*[[Non-Standard Residues]]		*[[Non-Standard Residues]]