Displaying Spectra
Clicking this button updates the spectral windows with the information from the current connection. Recall that smartnotebook does not do the update, it invokes nmrview routines with the proper information. In the first startup example figure, the hncacb spectrum of residue i-1 is on the left and the cbcaconnh and hncacb spectrum of residue i on the right.
Red and black cursors are placed on certain peaks which aid in visualization of the connection. If you click on the display button once, the cursors are placed on ca0, cb0 peaks. Double click the display button to have the cursors placed on ca1 and cb1.
It is important to note that the spectra used and how they are displayed is determined by a configuration file. Most users should not have to be concerned with the details on how this works. However if you are determined to customize your own spectral display, please see the developer's page.
The "Add to Chain" button can only be invoked when the currently selected
connection in the connection panel is appendable to the first
or last connection of the current chain. It also lights up when the
current chain is empty. Finally, this button also lights up when the
current chain consists of two or greater connections and the currently selected
connection can replace the first or last connection of the
current chain. This makes it convenient when investigating multiple
possible connections for an endpoint of a chain.
Clicking on "Add to Chain" causes the following events to occur:
The user selects the connection to delete in the Current Chain panel
and clicks the delete button. Note that you cannot delete a connection
from an assigned chain, you must un-assign the chain first. The events
which occur with a "Delete from chain" are similar to "Add to Chain" as
mentioned above.
You can only delete one connection at a time. Since deletion of multiple
connections at a time should be a relatively rare event, it is currently
not implemented in the current snb version.
The best fit button calculates the best place in the sequence to
assign the chemical shifts in the current chain. It invokes the
shift-analysis pop-up window at this position.
Smartnotebook defines the best place for assignment by trying to minimize
the worst fitting chemical shift to the target values in the chemical shift
file input. The calculation of each chemical shift fit (or test stat) is simply:
Question: What happens if the best place for assignment is already assigned?
I hope users do not find this annoying but snb does not care if the best
place for assignment is already assigned. Therefore, if the user wants to see
the assignment fit at a different amino acid, he/she will have to click on that
amino acid in the sequence panel . Again, my rationale
is that it is more important for the user to be alerted to potentially "better"
assignment possibilities as opposed to slight inconveniences from an additional
mouse click. If enough users disagree, I can be persuaded to change this.
This file last updated:
Questions to:
bionmrwebmaster@biochem.ualberta.ca
Add to Chain
Delete from Chain
Best Fit
abs((proposed shift(i) - expected shift(i)) / stddev shift(i)))
If this is too simplistic or problematic, please let me know.
Smartnotebook Home