Getting Unremediated PDB Files: Difference between revisions
Eric Martz (talk | contribs) corrected year to 2009 (3 places) and added introductory sentence at top of page. |
Eric Martz (talk | contribs) →Why would you need an unremediated version of a pdb file?: updated obsolete paragraph about Proteopedia |
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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. | ||
===How to get the unremediated version?=== | ===How to get the unremediated version?=== | ||