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
Molecule Chain: Selects which molecular chain to select and show residues from
Ccp Residue Code: Selects which kind of residue to display sequence and assignment information for
Shift List: Selects which shiftlist to get chemical shift values from
Print: Print the three-dimensional coordinate display to a PostScript, EPS or PDF file
Clone: Clone popup window
Help: Show popup help document
Close: Close popup