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Measure Differences Between Pairs of Chemical Shifts
This system is designed to calculate the differences between pairs of chemical shift values in two contexts: firstly directly comparing peak locations in related spectra and secondly by comparing averaged chemical shift values (averaged over potentially many peak locations) in two different shift lists. The former allows the comparison to be restricted to only certain peaks, i.e. those with common assignments in two peak lists, and gives an overall ‘shift distance’ for each peak, rather than just differences for the separate dimensions.
Peak List Comparison
Comparing peak positions is achieved with the functions presented in the first tab. In essence, the user selects two peak lists from the top pulldown menus and views the results in the table below. The “Atom Names” options allow the comparison to be restricted to only certain kinds of assignment. (The atom names have to be complete, no wild cards are allowed.) The “Scale Factor” values are used in the calculation of the “Shift Sum” and “Shift Dist” values so that positional differences in dimensions with dissimilar isotopes may be compared; the difference for a dimension is multiplied by the scale factor for its isotope type.
Shift List Comparison
The second tab simply takes two chemical shift lists, specified in the top pulldown menus and compares the values of the contained chemical shifts. Each row corresponds to one resonance that has a shift measurement in the two shift lists. The user may optionally filter the list by adding specific “Atom Names” so that only certain kinds of assigned resonance are compared. (The atom names have to be complete, no wild cards are allowed.) It should be noted that the values in shift lists are typically based upon an average of the assigned peak positions for resonances that use that list. Two different sets of experiments may be compared by allocating them among two separate shift lists; see the main Experiments option.
Sequence Alignments
When comparing peak lists or shift lists where assignments are made to two different but similar chains, the calculations can optionally use a sequence alignment. The sequence alignment that is used is presented in the third tab and represents a residue to residue mapping. Which chains are used in the alignment is automatically determined from those that are assigned in the selected peak lists or shift lists and at present only the highest scoring pair of sequences is considered. More fine-grain control may be added in the future.
Function Buttons
The lower function buttons relate to either the peak list or shift list comparison, depending on which is currently viewed. The [Make Shift Difference List] is handy to give a permanent record, stored in the CCPN project, of the calculated chemical shift differences. The shift difference lists are a kind of measurement list and are viewable at any time via the Measurement Lists table. If a measurement list is not made the only way to get the same shift differences again is to repeat the calculation. The [Show On Structure] is designed to colour a graphical structure display so that the size and colour of atoms is determined by the shift difference of their resonances - atoms without a shift difference are left at their default rendering.
Caveats & Tips
For investigating how chemical shifts differ when considering more than two peaks, e.g. when following how peaks move during a titration the Follow Shift Changes tool should be used.
To make a peak list that is based on averaged chemical shift values, which may be compared by this system, then for certain types of spectra the user may create a synthetic peak list. This is accessed via the Peak Lists popup option [Predict from Shifts].
Measure differences in chemical shifts by comparing peak positions
Peak List A: First peak list to use in comparison
Peak List B: Second peak list to use in comparison
Fully assigned only: Whether to compare positions for only fully assigned peaks
H,H1: Restricts the comparison to peaks assigned to particular kinds of atoms, in their first dimension
N: Restricts the comparison to peaks assigned to particular kinds of atoms, in their second dimension
Use Sequence Alignment: Whether to use the residue sequence alignment in the shift comparison
1.0: First dimension scaling factor use to compare shifts of dissimilar isotopes
0.15: Second dimension scaling factor use to compare shifts of dissimilar isotopes
Table 1 | |
Residue(s) | The residue assignment(s) of the peaks |
Reson. 1 | Resonance assignment in the first dimension |
Shift 1A | Chemical shift of first peak (A) in first dimension |
Shift 1B | Chemical shift of second peak (B) in first dimension |
Δ 1 (ppm) | Chemical shift difference in ppm for first dimension |
Reson. 2 | Resonance assignment in the second dimension |
Shift 2A | Chemical shift of first peak (A) in second dimension |
Shift 2B | Chemical shift of second peak (B) in second dimension |
Δ 2 (ppm) | Chemical shift difference in ppm for second dimension |
Shift Sum | Sum of the chemical shift differences in the two dimensions |
Shift Dist | The square root of the sum of the isotope weighted shift differences squared |
Seq Num | Sequence number of any assigned residue (for easy graphing) |
Measure differences in the chemical shift values from two shift lists
Shift List A: First chemical shift list used in comparison
Shift List B: Second chemical shift list used in comparison
Use Sequence Alignment: Whether to use the residue sequence alignment to compare dissimilar molecules
Atom Names: Restricts the comparison to only specific atom types, e.g. “HA, HB”
Table 2 | |
#1 | Serial number of first resonance |
#2 | Serial number of second resonance |
Assign Name | Assignment of resonance(s) |
Residue 1 | Residue assigned to first resonance |
Residue 2 | Residue assigned to second resonance |
Shift 1 | Chemical shift value of first resonance |
Shift 2 | Chemical shift value of second resonance |
Δ | Chemical shift difference, in units of the shift list |
The sequence alignment used to compare shifts between two different molecules
Table 3 | |
Residue | Residue in the first sequence |
Aligned Residue | Aligned residue in the second sequence |
Common Assignments | Names of atom assigned resonances common to aligned residues |
Show Peaks: Show a table of peaks corresponding/assigned to the selected rows
Update: Force a manual refresh of the shift difference calculation
Make Shift Difference List: Save the results in the CCPN project as a data list
Show On Structure: Show the shift difference results on a graphical structure display