Search Button

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• Residue ID constraints
• Atom constraints
• Probability score

1. Scroll the amino acid list of the ResID(i-1) atom constraints window and click on the S-ser button. The software finds the first SER in your sequence and places the associated atom constraints in the boxes (eg 52.21 >= ca >= 64.93).

2. For the amino acid list of ResID(i) click on "Any" to indicate there are (virtually) no constraints on the second amino acid.

   

3. Click Search in the search window. The software tells you there are 17 hits and those connectivities are displayed in the connections panel as shown below.

   

1. In the ResId(i-1) window, click on the K-lys menu item until LYS:120 is displayed. In the ResId(i) window, click on G-gly menu item until GLY:121 is shown. Note that the 'cb' atom is not applicable and is darkened. Click the "Search" Button and this time 42 connectivities are possible.

   

   Note: Since most users will use default shift constraints files where amino acids of a certain type have identical constraints, it is only necessary to click on the desired amino acid once.

1. (Optional) Set the "Reference Id" to 1. This means our current set of connectivities involve reference ID 1.

   

2. Click the Search button and select the menu item "Next Un-assigned". Click the menu item "Any" for both Atom Constraints panels and press "Search".

   

3. The output in the main snb panel indicates that Reference Id 2 is the next unassigned reference peak and there are 3 possible connectivities. As you continue to click on "Search" you quickly parse through your connections looking for ones that look promising for chain building.

You can use a similar procedure to parse in the other direction (eg, Prev Un-assigned ). Users may have a number of chains, some of which are not yet assigned. So rather than looking for the next un-assigned peak, it is more useful to see which reference peaks are not found in any current chain (eg, Next Un-used button).

More Notes

1. The lower and upper bounds of residue atom constraints are determined by the value of the "stddev limit on assignment" which is shown whenever you click the "best fit" button.

2. The box 'Any' represents no shift constraints.

3. Since all results from searches are sorted based on connectivity score, it is not clear whether the Probability Score constraint is necessary. It is possible that users may want to view all connections that have some high minumum probability score and look at these as possible starting points for building chains (eg, the data is poor and you are only going to get limited assignment information).

4. Users can manually set the constraint boxes. However you can define your own default atom constraints in the lib/experiments/*/*.search file. The format is pretty straight forward. It is probably best to edit a copy of the file in your current working directory and then modify the snb.init file to point to the new file location.

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