The "Inspector" is a multi-functional tool for performing a number of operation on peaks 
and peaklists. A more indepth description can be found here.

1. Calculate: This option will calculate the median line width for each dimension of each
peaklist and set the tolerance to that value.

2. Set To Defaults: This option uses the default set of tolerances for each dimension.

3. Set To User Values: This option allows the user to overwrite the default values 
with values set by the user. These values will be applied with the "Setup" button.

1. C toggles on or off any row which has the Y axis set to the carbonyl chemical shift 
range.
2. Hali toggles on or off any row which has the Y axis set to the aliphatic H chemical
shift range.
3. CA toggles on or off any row which has the Y axis set to the CA chemcial shift range.
4. CB toggles on or off any row which has the Y axis set to the CB chemcial shift range.

1. Show Ref Chart: Opens a separate window that displays the HN plane for the "Reference
List" experiment (usually the HNCO). The displayed peak is the amide proton/nitrogen 
crosspeak for residue *i* and corresponds to the peaklist numbering in the HNCO peaklist.
The crosspeaks can be advanced using the forward and back arrows. The peak number will 
change to an assigned value upon confirmation of the assignment into the protein sequence.

2. Align: Allows for alligning cross peak chemical shifts that are slightly off in the 
referencing between the various experiments. This action seeks to line up the chemical
shifts for cross peaks onto the amide proton/nitrogen cross peak of the HNCO experiment
so that the chemcial shifts of all correlated peaks are within the tolerances specified.
The chemical shift referencing of peaks in the alligned peak lists are then updated to 
reflect the changes. 

3. Filter: This action seeks to filter out spurious peaks and artifacts. Filter compares 
each peak list to the "Reference" list (HNCO) and removes peaks that do not match 1H and
15N chemical shifts founf in the reference list. When filtering, RunAboutX looks at whether
a peak is within 2 times the tolerance value of a reference peak and if not that peak is
deleted from the list. The increase in tolerance value minimizes the risk of erroneously
removing peaks that are valid but slightly misalligned.

4. Assemble Spin System: This action will group together peaks from peaklists that contain 
the same amide H and N chemical shifts as found in the HNCO experiment. This effectively 
determines which peaks in different peak lists belong to the same residue or "cluster"

5. Assign Atom Types: This action examines each cluster and attempts to assign the cluster  to 
a given amino acid type. This action also seeks to determine which cross peaks belong to
residue *i* or to residue *i*-1. The conection between clusters based on the identity of 
a crosspeak going back to residue *i*-1 is given by a green line between the current 
cluster being examined and the previous cluster (to the left). A blue line between cross
peaks indicates a connection between a cluster and the successive cluster.

6. Match Adjacent: This action seeks to link up clusters in a way that the peaks
can be assigned to amino acids in the protein sequence. At this point in the analysis the
clusters can be more correctly thought of as spinsystems that are linked into the amino 
acid sequence. Important aspects of the Helm after the "Match Adjacent" action are taken
are shown below:

The cluster under current inspection is shown in the window (1). In this example it is 
cluster 19 and the chemical shifts for the current cluster are given by the capital 
letters designating the amide H, N, the carbonyl (C) and the CA and CB with the chemical
shifts given for each atom (blue box). The cluster being analyzed can be advanced using
the arrows or by clicking on any cluster in the linear display of clusters. 
The best match on the N-terminal side *i*-1 is
given on the left side, in this example cluster 47 (2) and the lower case letters 
designating the carbonyl (c) and the ca and cb with the chemical shifts given for each
atom (red elipse). The best match for the C-terminal side *i*+1 is given on the right
side, in this example cluster 21 (3). The match probability is given by a score which
spans +100 to -150 where -150 is the highest probability and +100 very low probability.
For the current cluster the best fit for amino acid spin system is given by the list of 
amino acids (4). Amino acids in capital letters have a higher probability of a match
for the current cluster spinsystem. The probability is highest for a letter in lighter
background. White background is a very high probability match and for this example,
cluster 19 is best matched to a spinsystem for threonine (CB = 70.2 ppm, CA = 60.3).
Hovering the mouse pointer over the chemical shifts for each atom in either the *i*-1 
or *i* cluster gives the average of chemical shifts for the atom type from the peak
position from all of the experiments where that peak is found. The deviation from the 
average is also given. In cluster 47 the *i*-1 ca has a chemical shift of 52.8 ppm that is
derived from values from 3 different experiments and has a deviation of 0.2 ppm from the 
average. The row of chemcial shifts below each atom chemical shift is how well the chemical
shift for a given atom match between the *i*-1 and *i* experiments. Chemical shifts that 
match exactly show complete agreement between for example the CA shift from the HNcoCA 
experiment and the HNCA experiment. If these numbers are different by more than the 
specified tolerance for that atom type the lower value appears as magenta.

1. ALL: Provides a list of all clusters after the "Assemble Spin Systems" action. 

2. CORRECT: Lists all cluster that contain the correct number of peaks between the *i*-1
and *i* clusters.

3. LONELY: After the "Assign Atom Types" action clusters may be created that contain only one
or two peaks in the cluster. These spurious clusters are deemed "lonely" and can be 
removed from the cluster list by clicking the circle with the slash.

4. MISSING: Lists all clusters that are missing one or more of the inter and intra-residue 
connections. 

5. MISSING_PPM: After the "Assign Atom Types" action this menu option lists all clusters that 
have missing inter and intra residue connections and lists which chemical shift is missing.

6. EXTRA: Lists all clusters that contain additional inter or intra-residue connections.

1. Split: Divides a cluster into two (creates another cluster number at the end of the 
current enumeration) if the original cluster contains two peaks in the reference experiment
(HNCO) and or there are a large number of extra peaks over which is expected (i.e. 20 peaks
where 11 are expected). Overlap in the reference experiment is the biggest cause of
additional peaks. If a peak is assigned to the new cluster and it should belong in the 
original cluster then clicking on the peak and choosing "Move to Cluster" it will reassign
to the original cluster.

2. Move to Cluster: Will move a selected peak to another cluster (how to choose the cluster
where the peak is being moved to?)

3. Analyze: Performs the action that "Assign Atom Types" provides. Use "Analyze" to correct a
cluster if the atom patterns have been missassigned. 

4. GraphMatching: Opens a popup window that contains controls for automatically assigning
the clusters and updating the Atom Table with chemical shifts for each residue. The popup
appears as shown below:

The controls along the top are:

1. Match: Begins the process of autoassigning using the specified parameters.

2. Stop: Once Matching begins this control allows the user to stop the process prior to 
the maximum number of tries.

3. Details: 

4. Reset: Resets the results and allows the user to change parameters for another try.

5. Assign: Updates the Atom Table with chemical shifts for each residue assigned. Updates
the Helm to display the clusters that have been assigned to the residues.
After a successful matching the popup looks as follows:

Parameters for the Graph Matcher are as follows:

a. N Tries: The total number of tries for the genetic algorithm

b. Population Size:

c. NGenerations:

d. Mutation Rate:

e. Crossover Rate:

f. Fraction Match Requirement:

g. N Steady:

h. SDev Ratio:

i. Max Age:

j. Elite Number:

A check box for selection of "Mutation Profile" is provided which toggles on or off the 
selection of:

The progress of the assignment process can be monitored using the "Status" values which
reports on each "Try" of the total "N Tries" parameter and within each try the "Gen" or 
generation being evaluated. The score for the current generation being evaluated is given
in the "Current" fierld while the "Best" gives the best score (most negative number) to
that point in the analysis.

5. Trim: This tool looks at each cluster and all peaks associated with it and determines 
how many peaks are expected to appear for each cluster for a given experiment type (i.e.
HNCACB. If there are more than the expected number of peaks, the weakest peaks are trimmed
from the cluster. (is this different from the previous documentation)?

Expected number of peaks per cluster for Residue *i*-1 to Residue *i* if using the 
HNcoCACB/CBCACONH experiments:
        *i*-1   ,   *i*
    non-Gly non-Pro, non-Gly = 11
    Gly non-Pro, non-Gly = 9
    non-Pro non-Gly, Gly = 10
    non-Pro non-Gly, Pro = 0

Expected number of peaks per cluster for Residue *i*-1 to Residue *i* if using the 
HNcoCACB/CBCAcoNH experiments:
        *i*-1   ,   *i*
    non-Gly non-Pro, non-Gly = 12
    Gly non-Pro, non-Gly = 10
    non-Pro non-Gly, Gly = 11
    non-Pro non-Gly, Pro = 0    

6. Trim All: This tool trims all weak peaks from clusters so that the expected number of 
peaks for each experiment type is met.

7. Extend: Automatically extends the cluster matching if the score is good and the RAV 
(R = Recipricol both cluster *i*-1 -> *i* and *i*-1 <- *i* both match well), 
(A = Availability a particular cluster has not already been matched and confirmed with 
another cluster), (V = Viable a cluster is viable with another if three or more carbon
frequencies match one another across spectra and the proposed pair exhibit chemiscal 
shifts conistent with a pair of residues in the protein sequence) is matched. Extend
will arrange the extended matched clusters and color codes them.    
8. Extend All: Examines all clusters and attempts to assemble all available clusters that
can be matched and confirmed. 

9. Freeze: If a fragment of matched clusters (same color clusters) looks to be well placed
in the amino acid sequence (dark green bars underlining the amino acids) choosing the
"Freeze" option will map the two. After the "Freeze" option is used both the cluster group
and the amino acid sequence will adopt the same coloration and will be bounded on the top
with a dark line.

10. Thaw: Reverses the "Freeze" action for a given stretch of clusters.

11. Thaw All: Reverses all "Freeze" actions.

1) Assemble and Combinations: The dashboard appears as follows after the "Assemble Spin
Systems", "Assign Atom Types" and "Match Adjacent" actions have been taken. 

The clusters have been "assembled" and appear in a linear row. The check boxes adjacent to
the RAV color bars allow for the "Confirming" of the match for cluster *i* to cluster
*i*-1. Upon confirming the connection the cluster list is reorganized and the confirmed 
clusters are colored. In addition sections in the amino acid sequence are highlighted that
match the cluster chemical shifts for given amino acid residues that are sequentially 
situated. The best match is underlined with a darker color.