Temperature value: Difference between revisions

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==Missing Residues==

Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. [[FirstGlance in Jmol]] (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) has ~~a '''Gaps''' button (~~under ''~~Key Resources~~''~~) that explains how to detect and visualize missing residues~~. Alternatively, at the [[PDB]], the ''Sequence'' tab provides a graphic representation of the sequence that indicates gaps in two ways. First, the thin black line underneath the sequence is broken; second, touching a residue above breaks in the line reports "no identifier from ATOM record (no structural data available)". However, it is easy to overlook breaks in the line, ~~while~~ the ~~[http://molvis.sdsc.edu/fgij/notes~~.~~htm#seq method in~~ FirstGlance in Jmol~~], which relies upon~~ the ~~[http://dunbrack.fccc.edu/Guoli/s2c/ SEQRES to Coordinates alignment server of Wang and Dunbrack], offers a reliable way of finding~~ every ~~gap~~.

Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. That is, these residues were present in the crystallized protein, but have no coordinates in the atomic model because their electron densities were too indistinct.

[[FirstGlance in Jmol]] (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) lists missing residues and marks their positions with eye-catching "empty baskets".

The sequence listing for a PDB code offered by [http://pdbe.org/ PDB-Europe] makes it easy to see missing residues: they are highlighted with a gray background. FirstGlance in Jmol has links to these listings under ''Sequences''.

Alternatively, at the [[PDB]], the ''Sequence'' tab provides a graphic representation of the sequence that indicates gaps in two ways. First, the thin black line underneath the sequence is broken; second, touching a residue above breaks in the line reports "no identifier from ATOM record (no structural data available)". However, it is easy to overlook breaks in the line.

In addition to entire residues missing from the atomic model, side chains atoms may be missing (due to disorder), even when the main chain atoms are present. FirstGlance in Jmol puts the label '''S-''' on every residue with missing side chain atoms.

==Data Format==

Temperature value: Difference between revisions

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@@ Line 36: / Line 36: @@
 ==Missing Residues==
-Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. [[FirstGlance in Jmol]] (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) has a '''Gaps''' button (under ''Key Resources'') that explains how to detect and visualize missing residues. Alternatively, at the [[PDB]], the ''Sequence'' tab provides a graphic representation of the sequence that indicates gaps in two ways. First, the thin black line underneath the sequence is broken; second, touching a residue above breaks in the line reports "no identifier from ATOM record (no structural data available)&quot;. However, it is easy to overlook breaks in the line, while the [http://molvis.sdsc.edu/fgij/notes.htm#seq method in FirstGlance in Jmol], which relies upon the [http://dunbrack.fccc.edu/Guoli/s2c/ SEQRES to Coordinates alignment server of Wang and Dunbrack], offers a reliable way of finding every gap.
+Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning any atomic positions at all, leading to '''missing residues'''. That is, these residues were present in the crystallized protein, but have no coordinates in the atomic model because their electron densities were too indistinct.
+[[FirstGlance in Jmol]] (linked beneath the molecule on every [[PDB code]]-titled page in Proteopedia) lists missing residues and marks their positions with eye-catching "empty baskets".
+The sequence listing for a PDB code offered by [http://pdbe.org/ PDB-Europe] makes it easy to see missing residues: they are highlighted with a gray background. FirstGlance in Jmol has links to these listings under ''Sequences''.
+Alternatively, at the [[PDB]], the ''Sequence'' tab provides a graphic representation of the sequence that indicates gaps in two ways. First, the thin black line underneath the sequence is broken; second, touching a residue above breaks in the line reports &quot;no identifier from ATOM record (no structural data available)&quot;. However, it is easy to overlook breaks in the line.
+In addition to entire residues missing from the atomic model, side chains atoms may be missing (due to disorder), even when the main chain atoms are present. FirstGlance in Jmol puts the label '''S-''' on every residue with missing side chain atoms.
 ==Data Format==