All of the below requests/issues have been addressed for the new release.
Specific comments follow.
> 1.) It would be good if when I clicked on a Query spin system (and it
> moves to that spin system in the query window and potential links in the
> target window) if it could track on the HSQC window as well and mark the
> peak that is the query. I am not sure if it used to do this but it
> currently does not for me.
In the new version the user simply selects an HSQC root window (or none)
in the Query Windows and Spectra section.
> 2.) I also think it would be good if there was a new button that when
> pressed popped up another window that showed strips of all the spin
> systems in that linked stretch. "Finally, it is very nice how it gives
> you potential "Sequence locations" of stretches of sequential spin
> systems. It would be even nicer if it was possible to press a button
> here to show these sequential spin systems in a strip view. i.e.
> i+2,i+1,i,i-1,i-2 in 5 strips in the same window (preferably without
> horizontal strips). I would find this visual queue very useful."
There is now a [Strip] button for the Sequence Locations, noting that this
works with the "match" window, which is likely to be the one with the
space. Prolines will be included as blank panels, so you know there's an
hiatus.
> 3.) One thing I noticed was that if I add a new peak I need to reload
> the popup for all the features to work. That is if I add a new peak I
> can "Set seq link" to it but I cannot press "Goto i-1" to move to that
> peak until I reload the popup. Obviously closing and reopening the popup
> is not a major issue but it could be improved. Maybe a "refresh" or
> "reload" button on the popup could be added as a quick fix?
Many more event notifiers have been added. The sequential assignment
system will thus respond to: moving peaks, changing peak intensity (e.g.
sign) and changing peak assignments (e.g. introduce a new peak). All
tables and matches for the systems should respond and update
automatically.
> 4.) I would also find it useful to have a "Deassign Selected" button to
> complement the "Assign Selected" button that deassigns the whole of the
> linked stretch of residues. I dont know if this is possible (or if there
> is a reason why not to have it).
Now added.
> 5.) Finally, if I click "assign selected" so it assigns the whole strip
> of sequentially linked residues it would be useful if it pointed out
> that this region will run through a proline. I assigned a strip of
> around 10 residues where a proline was in the middle and it did not
> point this out and produced a proline amide peak (tho I forget which
> atom names it used). I think a prompt to suggest that such an assignment
> is almost certainly wrong would be useful.
So the first issue I have fixed is that no prolines should appear in the
"Sequence Locations" in the first place if they match a spin system with
an amide.
Secondly, I have added pre-assignment checks to warn if the sequentially
linked spin systems would go through a proline (or hydroxyproline) or fall
off the edge of the sequence. The user can optionally back-out of the
assignment in either case.
T.
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.ccpn.ac.uk
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