Tim points out that as well as the out-of-date tutorial on the old
website, there is also an up-to-date tutorial on the new website:
http://www.ccpn.ac.uk/ccpn/software/ccpnmr-analysis/tutorials/ccpnmr-analysis-basics/
which does cover the Link Peak Lists functionality (under the "Efficient
Resonance Assignment" section).
Wayne
On Tue, 3 Apr 2007, Wayne Boucher wrote:
> Hello,
>
> We could do with an FAQ-like documentation section which answers these
> basic questions for beginners. We're going to hopefully (somehow) get
> the community involved with this (because otherwise we would do nothing
> but documentation!). This should help. For now I would recommend
> beginners to go throught the tutorial.
>
> (At some point perhaps in October we ought to run another Analysis course
> in Cambridge for beginners.)
>
> On the specific question of 3D peak picking, I think there are currently
> several options:
>
> (1) pick manually (not recommended!)
>
> (2) zoom out to whatever region you want and use crtl-shift-left-drag
> (this is covered in the tutorial, which is linked in from the
> documentation)
>
> (3) use the region peak picker in Crosspeaks -> Region Peak Find (make
> sure the contour levels are set suitably first)
>
> (4) use the Assignment --> Link Peak Lists functionality to go from peaks
> in a 2D (e.g. an HSQC) to a 3D (this is also covered further down the
> tutorial that we have been using recently but is not in the version that
> is currently on the web).
>
> On the performance issue I suspect the users are better than us at this.
> We know we need to improve the refresh issues (too many redraws are being
> done) and there are still probably memory leaks to sort out. Using native
> OpenGL drivers seems to be the best option. And 1 or 2 Gb of memory is
> bound to help. And the more recent the Python the better results you will
> get as well (they get reasonable speed improvements every release).
>
> I would recommend not using NmrPipe data because it is not blocked (at
> least as I have seen it, others might be able to correct me on this
> impression), which makes it slow. First convert it to one of the other
> formats (all of which should be fairly equal in performance, since it's
> the blocking that matters).
>
> Wayne
>
> On Tue, 3 Apr 2007, Paul Driscoll wrote:
>
> > Hi Guys,
> >
> > Playing devil's advocate for new users... does this information contain
> > anywhere the information 'How to pick peaks in a 3D spectrum'? Someone in
> > my group tried to find this, could not, worked out a way to do it that may
> > well not be optimal, found it took 2-3 hours for a straightforward
> > (small protein) triple resonance data set and now has the opinion that
> > they want to revert to ANSIG as this was much quicker. Are we
> > missing something?
> >
> > On a related matter, that is inspired in part by the recent discussion of
> > OSX implementation performance issues... Is there a recommended hardware set
> > for CCPN software on PC/linux platforms? Where are the real bottlenecks?
> > Is it all in the graphics card?
> >
> > [Also is there a performance difference when reading in different spectra
> > formats - e.g. AZARA vs. NMRPIPE?]
> >
> > Paul
> >
> >
> > On Mon, 2 Apr 2007, Wayne Boucher wrote:
> >
> > > Hello,
> > >
> > > Yes, our wonderful new website is Plone-based and we have yet to figure
> > > out how to insert an entire directory of webpages inside it (great, eh).
> > > But it is still available on the old website at:
> > >
> > > http://www.bio.cam.ac.uk/nmr/ccp/analysis/
> > >
> > > and it is also available on the documentation in the release. If you open
> > > the index.html file in WHERE_YOU_UNPACKED_CODE/ccpnmr/doc and then click
> > > on the CcpNmr Analysis documentation link you should arrive at the same
> > > thing (up to recent changes...).
> > >
> > > Wayne
> > >
> > > On Mon, 2 Apr 2007, Vicky Higman wrote:
> > >
> > > > Hi,
> > > >
> > > > I discovered today that the 'menu options' and 'popup guide' parts of
> > > > the CCPN Analysis documentation don't seem to be on the new set of web
> > > > pages. We've got several people who are just starting to use Analysis in
> > > > our group and it would be nice if they could access these web pages. Are
> > > > they still available under some other (possibly old) URL?
> > > > Thanks.
> > > >
> > > > Vicky
> > > >
> > > >
> > > > --
> > > > ****************************************************
> > > > Dr. Victoria A. Higman
> > > > Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
> > > > NMR-Supported Structural Biology
> > > > Robert-Roessle-Str. 10
> > > > 13125 Berlin
> > > > Germany
> > > > Phone: +49-30-94793 223
> > > > E-mail: [log in to unmask]
> > > > ****************************************************
> > > >
> > >
> >
> > --
> >
> > Paul C. Driscoll
> > Professor of Structural Biology
> > ---------------------------------------------------------------------
> > Prof. Paul C. Driscoll |Office (answer)phone: (44)-20 7679 7035
> > Dept. Biochem. & Mol. Biol. | Department fax: (44)-20 7679 7193
> > University College London | [log in to unmask]
> > Gower Street, London WC1E 6BT| http://www.biochem.ucl.ac.uk/~driscoll
> >
>
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