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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 >