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
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