Molecule : Residue Information

Residue Assignment Information

This popup is designed to give an alternative view of residue assignment status to the Atom Browser. The idea is that the user selects a particular molecular chain from the upper-left pulldown menu and then a type of residue from that chain in the adjacent pulldown. The left hand table then shows all the residues of that type within the selected chain’s sequence.

The left hand table lists residues of the selected type in the middle column. The first and last columns show the previous and next residue in the sequence for each central residue, thus showing a little of the sequence context for the selected kind of residue. If a row of this table is clicked, the central “i” residue is selected and the assignments are displayed in a 3D structural view in the right hand panel.

The right hand panel contains a structural display for the kind of residue selected, using idealised coordinates; not coordinates from a particular structure. With the “Show Assignment” option selected, this 3D view has the chemical shifts of the assigned atoms within the selected residue superimposed in the view. The chemical shifts are listed after the name of each atom, but naturally only if it has a resonance assignment in the selected shift list.

It should be noted that where atoms are deemed to be equivalent, like the three hydrogens in a fast rotating methyl atom set, the same chemical shift values will be used for all of the atoms within the set, although strictly speaking the value only really applies to the set as a whole. Also, for assignments that are non-stereospecific, e.g. there may be an assignment to Ser HBa which doesn’t commit to either HB2 or HB3 specifically, the display will show both possible chemical shift values (should they exist) for a given atom. For example, a Ser HB2 atom may be labeled as “HB” 3.72/3.85” because it potentially relates to either the “HBa” resonance at 3.72 ppm or the “HBb” resonance at 3.85 ppm.

3D View Controls

To move and rotate the three-dimensional residue display the following keyboard controls may be used:

  • Rotate: Arrow keys
  • Zoom: Page Up & Page Down keys
  • Translate: Arrow keys + Control key

Or altenatively the following mouse controls:

  • Rotate: Middle button click & drag
  • Zoom: Mouse wheel or middle button click + Shift key & drag up/down
  • Translate: Middle button click & drag + Control key

Atom Browser: BrowseAtomsPopup.html

Main Panel

pulldown Molecule Chain: Selects which molecular chain to select and show residues from

pulldown Ccp Residue Code: Selects which kind of residue to display sequence and assignment information for

pulldown Shift List: Selects which shiftlist to get chemical shift values from

button Print: Print the three-dimensional coordinate display to a PostScript, EPS or PDF file

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

None Information

Table 1
i-1 Identity of the previous residue in the sequence
i Locations of the selected kind of residue, considering the selected molecular chain
i+1 Identity of the next residue in the sequence

Atom Information & Idealised Structure

check CheckButton: Whether to show chemical shifts of assigned atoms

*None*: How many residues of the selected kind are assigned out of the total number available

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