> Under the "edit assignment" pop-up, I click on the "set atom type" but
> when I click on the correct atom (e.g., 574MetHg) on the "browse atoms"
> pop-up, this input is not reflected on the assignment in the "edit
> assignment" pop-up. This has only happened a couple of times and I am
> not sure why. Usually, I can set the atom type.
Hi Elizabeth,
I'm not exactly sure how you're doing things, but your description gives a
hint at what might be going on. Setting the type only means to set the
_kind_ of atom, i.e HA, CB etc, whatever the residue may be. Thus, we
allow you to choose any atom of the right kind from anywhere in the
sequence. If you know exactly which atom you want to assign then the left
most "Assign ..." button in Edit Assignment is the best route; this will
assign the spin system to a residue when required. Nevertheless, setting
the atom type for a resonance sometimes causes it to be fully assigned,
but only if the spin system is already assigned to a particular residue
and the atom name is known in that residue.
Even if you set the atom type of a resonance without any known residue for
the spin system there ought to be an indication of the type in the
displayed name for the resonance like "HA[123]". If you think there is a
persistent problem with Analysis it may be best to send us some screen
shots.
> Also, I am unable to make assignments to some of my NOE peaks under the "Link
> NOE resonances." I assume that every assigned residue should have an NOE to
> at least one other atom. Hence, I am surprised that under the "possible
> assignments," not all NOE peaks have listed option(s) when clicked. Perhaps
> this is as it should be, but I am not certain.
A few possibilities spring to mind here:
There could be chemical shifts missing in the assignment; the system
cannot suggest the cause of a peak if it is due to resonances that have
not been identified elsewhere.
It is possible that resonances have moved slightly and the tolerances are
too tight to find a match.
It is possible that not all of the known chemical shifts are in the shift
list that the NOE experiment is using; a quick check of the Experiments
table will show if this is so.
The peak could be aliased and so not at its real ppm value (only a
problem if "Aliased Possible" is off or if spectrum referencing is awry).
An outside possibility is that you are using a guide structure that has
some atoms missing (and so a distance cannot be measured).
Lastly, given certain popup window names it seems that you are using a
slightly old version of Analysis. Some problems may be resolved by using
the newest version (which is the version we regularly post fixes for)
Regards,
Tim
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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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