Temperature value: Difference between revisions
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==Missing Residues and Atoms== | ==Missing Residues and Atoms== | ||
===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'''. 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. | 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". | [[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". See snapshots at [[Missing residues and incomplete sidechains]]. It is much easier to overlook missing residues, especially at the ends of chains, in other molecular viewers such as PyMOL, ChimeraX, MolStar, and iCn3D (see [[Missing residues and incomplete sidechains|comparision snapshots]]). | ||
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''. | 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''. | ||
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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. | 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. | ===Incomplete Sidechains=== | ||
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 making this obvious. PyMOL, ChimeraX, MolStar, and iCn3D leave their users unaware of these missing atoms (see [[Missing_residues_and_incomplete_sidechains#Incomplete_Sidechains|comparision snapshots]]), which are especially important when looking at charge distribution or calculating electrostatic potential maps (see [[Missing_residues_and_incomplete_sidechains#Do_incomplete_sidechains_matter.3F|examples]]). Solutions are to use the AlphaFold model (where no atoms are missing) or to add back the missing atoms, use the free [https://www.protein-science.com/ Protein Repair & Analysis Server]. | |||
In the [[PDB file format]], missing residues are listed in REMARK 465, while missing atoms are listed in REMARK 470. | In the [[PDB file format]], missing residues are listed in REMARK 465, while missing atoms are listed in REMARK 470. | ||
