 |
 |
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 Tim points out that as well as the out-of-date tutorial on the old 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