Resonance: Spin System Types
This popup can be used to predict the residue types of spin systems in the project. All the residue type predictions are based upon the chemical shifts of the resonances within each spin system. These shifts are matched to the distribution of known chemical shifts in the BMRB database to create typing scores (see also Resonance: Reference Chemical Shifts). There are two ways of performing a prediction:
To predict on an individual basis for a selected spin system. This option is accessible by selecting a spin system and using [Show individual classification] button, which opens the Spin System Type Scores popup.
To predict the types of many spin systems at once. This method takes into account that the classification of one spin system affects the classification of another because there are a limited number of residues of each type in the sequence. The global spin system typing calculation uses a Monte Carlo algorithm to search for the top scoring mappings of residue type to spin systems. The search considered the shifts from one shift list and the residue types represented in one protein chain. This option is run with selected parameters using the [Run Typing] button.
The Resonance: Spin System Types popup.
Chain
Specifies the protein chain to which the considered spin systems correspond to. It is assumed that the residues of the selected chains are the only possible matches to the considered spin systems.
Shift List
Specifies which chemical shift list (and hence conditions) is used to provide the chemical shift information for the spin system type prediction.
Options
This section lists the options for the global Monte Carlo spin system typing prediction.
Keep existing types?
If selected, any existing assignment of spin systems to a residue type will be preserved as much as possible during the prediction. The spin system prediction is not guaranteed to be the same as the existing assignment if it strongly contradicts the overall high scoring type predictions.
Assignment threshold
Specifies the minimum score that is required for a spin system, with a unique classification within the global typing ensemble, to be assigned to the predicted type.
Ensemble size
Specifies how many top scoring global spin system to residue type mappings are considered in the calculation. These top scoring mappings (sequences) are used to check the consistency of residue type prediction for each spin system.
Num Search Steps
Specifies the number of steps in the Monte Carlo search used to find the best residue matches to spin system chemical shifts. The default number is 100,000 which was tested to be sufficient for a 10 kDa protein.
Isotope shifts to consider
Specifies which isotopes should be used in the prediction. Options are:
1H
13C
15N
Note that 13C chemical shifts are the most important chemical shifts in predicting amino acid types.
Spin Systems
This table lists all of the spin systems in the current project that can be considered for residue type prediction. It displays any currently assigned typing and the results of the global residue type prediction calculation.
Spin Systems table
This table lists all of the spin systems in the current project that can be considered for residue type prediction. It displays any currently assigned typing and the results of the global residue type prediction calculation.
#
The spin system serial number.
Residue
Displays the existing residue type or sequence assignment of the given spin system. These assignments will not have an influence on prediction if the [Keep existing types?] option is not selected.
Use?
If set to 'Yes' the individual spin system will to be considered for global residue type prediction.
Score
This is the resulting score after a global prediction run of the residue type match for the individual spin system. It is this value that is compared to the [Assigment threshold] (set above) when determining if the spin system should be assigned to its predicted type. Note that this value reflects the goodness of match of a residue type to the individual spin system's chemical shifts; it does not represent the global fit.
Types
The predicted spin system types (if any) that the spin system is predicted to be. If there is only one predicted spin type after a typing run then the spin system may be assigned to the predicted type using the [ Assign Types ] button (below).
Shifts
Shows a list of all the chemical shifts of the resonances in a spin system for the selected isotope type(s).
Run Typing
This starts the global spin system type prediction for the selected spin systems (those with [Use?] set to 'Yes'), which represent residues of the selected protein chain. The progress of the prediction is monitored in the Highest scoring mappings popup.
Assign Types
This button lets the user assign the high scoring spin systems to their predicted residue type, after the global residue typing calculation has run. The assignment is only made for a spin system if it was considered in the last typing run, has a best match with a score below the input assignment threshold and has only one predicted spin system type in the global typing ensemble.
Show Individual Classification
Allows the user to predict a selected spin system on an individual basis using the Spin System Type Scores popup. The prediction of the residue type of the selected spin system is done by only considering the shifts of the individual spin system, without the other spin systems having any influence.
Show Peaks
This option opens the Peaks: Selected Peaks popup to display all of the peaks that are assigned to any of the resonances present in the currently selected spin system.