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Hello Sara, I'm afraid that although we at CCPN work closely with the ARIA team in Paris, we're not the same people! We know that ARIA 2.3 does work well with the latest Analysis, but to receive a copy of ARIA you will have to contact the ARIA developers: http://www.pasteur.fr/recherche/unites/Binfs/aria/ Sorry about that, Dan On 26 Feb 2010, at 03:25, Sara Smith wrote: > Hi, > > I would like to work with ARIA 2.3 to work directly with CCPNMR Analysis 2.1.3 data project as Julien mentioned, but it does not seem to be available yet. When is ARIA 2.3 available and where? > > Thanks, > Sara > > > > On Wed, Feb 24, 2010 at 5:34 PM, Wayne Boucher <[log in to unmask]> wrote: > Tim's replies below. > > Wayne > > > On Fri, 19 Feb 2010, Julien Littérature wrote: > > Hi, > > I'm currently doing structure calculations and I have several questions. I'm new > to that, so sorry for non-ccpnmr questions. I used Analysis 2.1.3 to assign my > spectra. > > 1. When creating a new set of distance restraints, how is the Ref intensity > chosen? (is it just the average of all intensities?) How are methyls treated? > > > It is the mean of all intensities, but may exclude diagionals. This is a guess that works OK in most cases. ARIA & CYANA will recalibrate anyhow so the values are not so critical. The ref distance is setable nonetheless if user calibration is needed. > > > 2. In cns, what's the difference to have # instead of the OR statement between > all the atoms that are in a single noe peak (case B and A respectively, see > below)? > > A) assign (segid " A" and resid 40 and name HA) (segid " A" and resid > 40 and name HG12) 2.139 0.572 0.572 > or (segid " A" and resid 40 and name HA) (segid " A" and resid 40 > and name HG11) > or (segid " A" and resid 40 and name HA) (segid " A" and resid 40 > and name HG13) > B) assign (segid " A" and resid 40 and name HA) (segid " A" and resid > 40 and name HG1#) 2.139 0.572 0.572 > > If I output my data to in the cns format for distance constraints, it > automatically puts (for example) HBa and HBb as HB#, but it doesn't modify the > distance to take in account that it's the contribution from two protons. How can > we do that? > > 3. I tried working with aria2 and it worked well. Since aria2 is only compatible > with ccpnmr 1.0, what is the best practice to import the output data of aria2 > back in ccpnmr 2.0? I know how to import structures, but what do people do to > import the last unambig.tbl ambig.tbl and compare them to what was manually > assigned? > > > Best to use ARIA 2.3, when going through .tbl files the link to the peak is lost. > > Although, you can always peak::Peak Lists:Synthetic Lists:Make from Constraints which will allow you to see the ARIA assignments and navigate to the right spots in your spectra. > > > I tried the NMR Calculation item in the Other menu, but that doesn't seem to > work... (add new calculation group makes an error (I can send it later)) > > > This is only populated with ARIA 2.3. > > > 4. Small bug: I output my distance constraints to cns with FormatConverter, > using the "one line per constraint" option. If there's an OR statement at one > point, the next assignement is on the same line as the first (see the underlined > part below) and that makes an error in cns: > > assi ((selection1 )) (( selection2 )) 4.753 0.951 0.951 > or > (( selection1 )) (( selection3 )) assi (( selection4)) (( selection5 > )) 4.389 0.878 0.878 > > > Thanks, > > Julien > Daniel O'Donovan [log in to unmask]