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. | ||
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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. | ||
