This popup provides the user with an interface for connecting sequential spin systems using spectra that provide information about sequential backbone connectivities, such as:

• CBCAcoNH, which connects CB and CA resonances of residue i-1 with HN resonances of residue i.

• HNCACB, which connects CB and CA resonances of both residues i and i-1 with HN resonances of residue i.

• ....

In these spectra the dimension that contains the sequential and intra-residual connections is used for matching and indentifying sequential connectivities. The popup works in conjunction with spectra windows, in which query spin systems and their sequential matches are displayed for inspection. Identification of potential sequential links is aided by residue typing scores (see also Spin System Type Scores) and by calculating a combined score for fitting sequentially linked spin systems on the primary sequence of the protein.

Settings

The {Settings} tab allows the user to specify the 'Query' and 'Matches' spectra, spectrum windows, and a variety of peak matching parameters that are used in searching for and linking sequential spin systems. In case Query and Matches spectra are associated with the same spectrum window it can be convenient to clone the spectrum window in order to split the Query from the Matches spectrum window.

The Assignment: Link Sequential Spin Systems popup (Settings).

Query

This panel contains the options to select the Query window and spectra.

Window

Specifies the query spectrum window.

Spectra

This set of spectrum buttons allows the user to select multiple spectra for the query. Buttons of selected spectra are coloured.

Matches

This panel contains the options to select the Matches window and spectra.

Window

Specifies the matches spectrum window.

Spectra

This set of spectrum buttons allows the user to select multiple spectra for the matches. Buttons of selected spectra are coloured.

Peak Matching

In this panel the Peak matching parameters are specified.

Max Strips

Specifies the maximum number of strips to be displayed in the Matches window.

Tolerance

Specifies the chemical shift tolerance in the dimension in which peak positions in the query and matches spectra are being matched.

Auto Match

If selected, matching spin systems are automatically searched for when clicking on a spin system in the Spin Systems table of the {Spin System Table} tab. The matching spins systems are displayed in the Matched Peak Positions table of the {Spin System Table} tab.

Filter By Inter/Intra Type

If selected, the peak matches are filtered based on the connectivity type: inter or intra residual. 

Focus window views?

If selected, the spectrum windows focus on the matching peak positions by creating cells in which the peaks are focussed. The width of the cells in the dimension where connectivies are matched is defined by the [Focus width] parameter.

Focus width (ppm)

Specifies the width of the cells in the dimension where connectivies are matched if [Focus window views?] is selected.

Sequence

This panel lists the options for specifying the protein sequence used in the linking of sequential spin systems.

Chain

Specifies the chain used in linking sequential spin systems.

Spin System Table

The {Spin System Table} tab provides the interface where the user can select spin systems, find potential sequential matches and set sequential links for spin systems. Selecting a spin system in the Spin Systems table causes the Query and Matches spectrum windows to navigate and focus on the selected spin system and its matches.

The functionality in this tab allows the user to obtain probabilities for spin system types, and sequence locations of sequentially linked spin systems can be identified and assigned based on the residue type scores in the linked residues.

The Assignment: Link Sequential Spin Systems popup (Spin System table).

Spin System Table

This table lists the spin systems for which matches are searched for.

#

The serial number of the spin system.

Name

The name or assignment of the spin system.

i-1

The name of the spin system that has been linked to the current spin system as its i-1 neighbour in the sequence.

i+1

The name of the spin system that has been linked to the current spin system as its i+1 neighbour in the sequence.

i+0

The name of the spin system that has been linked to the current spin system as its i+0 neighbour in the sequence. DOES THIS MAKE ANY SENSE???

Seq, Segment

The sequential segment of the spin system.

Position

The position of the spin system in terms of the coordinates on axes orthogonal to the axis in which the connectivities are found.

Goto Next

Selects the next spin system in the Spin Systems table.

Goto Prev

Selects the previous spin system in the Spin Systems table.

Goto i-1

Moves the selection to the i-1 neighbour of the current spin system in the Spin Systems table.

Goto i+1

Moves the selection to the i+1 neighbour of the current spin system in the Spin Systems table.

Clear i-1 Links

Deletes the i-1 sequential links of the selected spin systems.

Clear i+1 Links

Deletes the i+1 sequential links of the selected spin systems.

Clear all links

Deletes the all sequential links of the selected spin systems.

Show Peaks

Shows the peaks of the selected spin systems in the Peaks: Selected Peaks popup.

Show Resonances

Show the resonances of the selected spin system in the Spin System Type Scores popup.

Matched Peak Positions

This table shows the positions of the matched peaks in the Matches spectra, and ranks the matches according to the best fits.

Rank

The rank of the matched peak positions according to the |Score| parameter.

Score

The score of the peak matches. The higher the score, the better the match. Note that the |Num Peaks| parameter must be considered as well in making the assignment: The more peaks match, the better the match.

Spin System

The spin system matching the query spin system.

i-1

The i-1 neighbour of the matching spin system.

i+1

The i+1 neighbour of the matching spin system.

Num Peaks

The number of peaks matching between the query spin system and teh matching spin system. The higher the number, the better the match is.

Find Matches

Finds and displays the matches of the spin system selected in the Spin Systems table.

Discard Selected

Deletes selected spin systems from the Matched Peak Positions table. The spin systems are only deleted from the table, but remain unaffected in the project. Using [Find Matches], previously deleted matches can be recovered in the table.

Set Seq Link

Sets the sequential link for the spin systems selected in the Spin Systems table and the Matched Peak Positions table.

Clear Rulers

Deletes all the rulers displayed in the Query and Matches spectrum windows.

Sequence Locations

This panel lists the sequence locations in the selected chain to which a series of sequentially linked spin systems can be assigned. A sequence location consists of 5 residues (i-2, i-1, i, i+1, i+2), with the central one corresponding to the spin system that is being analysed. Each time a spin system is selected, its assignment information, residue type and neighbouring residues are used to calculate the probabilities of the spin system and its neighbours matching a specific location in the protein sequence. Note that it is crucial that the spin systems are assigned to a type, or that they contain as many as possible atom type assignments to their resonances. The more atom type assignments, the more reliable the spin system type score is (see also Spin System Type Scores).

Rank

The rank of the matching sequence location. The lower the rank, the higher the probability that the given sequence location is the correct location in the primary sequence of the protein.

Score

The score of the sequence location assignment. The higher the score, the higher the probability that the given sequence location is the correct location in the primary sequence of the protein.

i-2

The name of the i-2 residue in the matching sequence location of 5 residues.

i-1

The name of the i-1 residue in the matching sequence location of 5 residues.

i

The name of the i residue in the matching sequence location of 5 residues.

i+1

The name of the i+1 residue in the matching sequence location of 5 residues.

i+2

The name of the i+2 residue in the matching sequence location of 5 residues.

Residue types

This panel lists the residue type probabilities of the selected spin system and its i-2, i-1, i+1 and i+2 neighbours. The residue type probabilities in the sequentially linked spin systems are used for calculating the score of the matching sequence locations, and thus help the user to make assignments of sequentially linked spin systems to locations in the primary sequence.

i-2

The residue type and corresponding probability score of the i-2 neighbour of the spin system selected in the Spin Systems table.

i-1

The residue type and corresponding probability score of the i-1 neighbour of the spin system selected in the Spin Systems table.

i

The residue type and corresponding probability score of the spin system selected in the Spin Systems table.

i+1

The residue type and corresponding probability score of the i+1 neighbour of the spin system selected in the Spin Systems table.

i+2

The residue type and corresponding probability score of the i+2 neighbour of the spin system selected in the Spin Systems table.

Assign Selected

Assigns the spin system selected in the Spin Systems table to the residue i in the sequence location selected in the Sequence Locations table.