On Tue, 3 Apr 2007, Wayne Boucher wrote:
> Tim points out that as well as the out-of-date tutorial on the old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).
Thanks for the hints.
>
> 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
> > >
> >
>
--
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
|
