Getting Unremediated PDB Files: Difference between revisions
No edit summary |
|||
| Line 10: | Line 10: | ||
===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. | 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> | ||
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. | 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. | ||