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.
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