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Hopefully now. Wayne On Tue, 14 Oct 2008, Johnny Croy wrote: > Wayne, > > The updates still aren't visible on the webpage. FYI. > > Johnny > > On Oct 14, 2008, at 10:20 AM, Wayne Boucher wrote: > > > Forgot, in case you don't know, the v2 download page is at: > > > > http://www.ccpn.ac.uk/ccpn/software/downloads-v2 > > > > Wayne > > > > On Tue, 14 Oct 2008, Wayne Boucher wrote: > > > >> Hello, > >> > >> We've just released v2.0.4 of the FormatConverter and Analysis (the > >> C and > >> Java APIs have not been released yet, but will be in the next few > >> days). > >> > >> This is mostly a bug fix release over 2.0.3 but there are some > >> added bits > >> of functionality, e.g. to do with structure display and shape > >> viewing. > >> > >> One thing that has been added to the installCode.py script is that > >> it will > >> automatically get all the latest updates. (In fact it doesn't even > >> ask > >> you if you want to do that, which has already caused me grief when > >> I was > >> testing the release, so I will change that when I remember to.) > >> Note that > >> this script is not run if you update from inside a current version of > >> Analysis. > >> > >> In terms of future releases, the next release of Analysis will > >> hopefully > >> have a fairly big data model change in it. Currently in Analysis > >> you have > >> one data model SpectrumWindow object corresponding to one window > >> popup > >> (for the contour drawing of spectra). This does not work so well > >> for how > >> we intend people to view and work with 1D shapes (of projection and > >> reduced dimensionality spectra), where we want different shapes > >> lined up > >> in frames on top of each other. This means the introduction of two > >> new > >> classes into the Analysis part of the data model. In the current > >> release > >> we instead have the equivalent ND spectrum being re-constructed on > >> the > >> fly. This is not ideal (and that code needs optimising). But I > >> imagine > >> most of you are not dealing with these kind of spectra yet! > >> > >> Wayne > >> > >> Below is a list of changes that Tim could remember that have happened > >> since v1.0.15 through v2.0.4. No doubt more has happened, but it > >> should > >> give you a reasonable idea. > >> > >> In LinkPeakLists, 3D windows are no longer mandatory for navigating > >> in > >> 2Ds. > >> Added ability to load PDB files for missing residues. Ability to > >> work > >> with structure ensembles throughout Analysis. > >> Added ChemicalShifts table for PostScript generation, etc. > >> Added DANGLE (dihedral angle and secondary structure prediction > >> based on > >> chemical shifts) > >> Old default CCPN macros now removed and replaced by options in > >> assignment > >> menu.Added editing of isotope labelling schemes. Added isotope > >> labelling > >> schemes to restraint generation, atom browser and predicting peaks > >> from > >> structures.Re-organisation of main menus.Unification of popups by > >> using > >> tabs. > >> Added the ability to display RMSD and residue validation results on a > >> structure.Added the ability to setup spectrometers and instruments, > >> with > >> which experiments were run. > >> Added Nexus, an automatic backbone assignment routine. > >> Linking sequential spin systems can now use 1H-correlation spectra. > >> Added user profiles. > >> Negative contour levels can be set separately from positive levels > >> now. > >> Added ability to update existing distance restraints in light of > >> new peak > >> assignments.Secondary chemical shifts now use sequence-dependent > >> adjustments. > >> In violation analysis added the proportion of ensemble violated, and > >> colour coded accordingly.When importing PDB structures, the PDB chain > >> codes and sequences are preserved where possible. Added Greek unicode > >> characters to atom browser. > >> Added ability to work with through space peak lists other than > >> NOESY, eg. > >> solid state experiments.Format Converter threading defaults to off > >> when > >> launched from Analysis. > >> Added ability to customise residue codes via profiles. > >> Added ability to load and describe reduced dimensionality / > >> projection > >> spectra. > >> Clicking on the structure viewer highlights the names of the selected > >> residue. > >> Analysis code re-organised into subdirectories. > >> Added icons for help, close and the new popup function, clone > >> (which makes > >> a new popup of the same sort). > >> Added ability to quickly add a sequence without having to go > >> through all > >> the complicated setup. > >> Added residue tab to Edit Structure popup. This displays phi/psi > >> angles, > >> RMSDs, validation results, etc. > >> When precisely placing peaks in pseudo-3Ds, they are displayed in all > >> visible planes. > >> Spin system typing much faster now. > >> Big revamp of Ramachandran plot and NOE matrix plot. > >> > > ------------------------------------------------------------ > Johnny Eugene Croy, Ph.D. > Research Associate > Wuttke Lab > > University of Colorado, Boulder > Department of Chemistry and Biochemistry > UCB 215 > Boulder, CO 80309-0215 > > Lab: (303) 492-2369 > Mobile: (303) 304-6069 > ------------------------------------------------------------ >