> I know little about structure calculation. Someone else is doing it for my
> protein. However i need to check the list of violations that Aria has given.
> what is the easiest way? I find an option violations under the "structure"
> pull down menu. How do i import violations? Further I also need to import
> some unambiguous assignments that aria has made.
There is no easy way to get violations back directly that I know of, but
maybe someone out there has some scripts...
In the upcoming ARIA2.1 violations, constraints and peak lists all go back
directly into the CCPN project.
In the mean time, for the violations it may be easiest to choose
structures from your ARIA run and let Analysis calculate the violations
for the input constraint lists. These are not as good as the official MD
violations, but it will hopefully get you most of the way there.
Also, although tedious you can work out which ARIA restraint (abeit for
analysing violations or making assignments) goes with which CCPN peak by
following the restraint numbers (this is set as the peak= value in the
.tbl file). These numbers are the serial numbers of the constraints in the
constraint list. So if you know which list you used you can find the
constraint that is being referred to in ARIA and thence go to the original
peak by using [View Peaks].
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.pantonia.co.uk
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