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CCPNMR  April 2006

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Subject:

new releases

From:

Wayne Boucher <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Mon, 10 Apr 2006 16:31:37 +0100

Content-Type:

TEXT/PLAIN

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Hello,

New releases for the FormatConverter (1.0.12) and Analysis (1.0.10) have
just gone live.  I've tinkered some more with installCode.py (hopefully
making things better, not worse), including asking about whether you need
to use 64-bit libraries on Linux.  The scripts in the bin directory now
have environment variables set directly, so you can (should) edit those if
need be.  For the Analysis release there is now also a pipe2azara script
in the bin directory.

Below are the changes (we could remember) for this release.  Let us know
(as usual) of any problems.

Wayne

Changes from 2006 Feb 03 (1.0.9) release to 2006 Apr 10 (1.0.10) release
Experiment series now use sample conditions. This change should be simple
but note that sample conditions essentially belong to experiments and
persist independently of experiment series. The condition type has changed
from "Time" to "delay time".

Make top module long and thin by removing Quit and Help buttons.

Added option to clone windows in Window -> Edit Window.

Added option to allow contour levels to be separated additively rather

Added option to run Python script on Analysis startup, by defining
ANALYSIS_STARTUP environment variable similar to the normal Python
PYTHONSTARTUP environment variable.

Added memory logging under Project menu. (Counts Python objects which have
not been garbage collected.)

Move Version from Project to new Help menu. Add About and Help to Help
menu.

Allow peaks to be "snapped" to local extremum (if for some reason they
have been moved away from this local extremum). It uses the boxWidth of
either the peak or the spectrum (the latter can be set in the dialog
Crosspeaks -> Peak Find Parameters) to determine how far to search, and
the peak is moved if and only if there is exactly one extremum in that
box. This is available either as a keyboard shortcut (P by default) or
under the right mouse menu Peak.

Added new option to main menu under Molecule, called Copy Chain
Assignments. You can use this popup to either transfer or duplicate
residue assignments between similar chains. This popup has the option to
copy on a per residue basis. Also, if duplicating assignments, the peak
assignments can also be duplicated

In the Assignment menu added Link Seq Spin Systems. This popup enables you
to setup search and query spectra for matching peak positions, e.g. as
used to do sequential C backbone assignments. In this case potential
sequential spin systems are displayed as strips. A selected spin system
can be linked sequentially, and appropriate resonances, spin system
groupings, etc., are automatically made.

Analysis now prints warning to the command shell if it finds proton
resonances which are bound to more than one other resonance, according to
atomic assignments and peak assignments, given 1-bond transfers.

Added a macro to AssignmentMacros to initialise HNCO or HNCOCA peak lists
in the same manner as initialiseHSQC.

The resonance browser now sets atom type for multiply selected resonances.

The constraint browser now does a violation analysis for distance and
dihedral constraints, given a structure. Also, there is the ability to
jump to the peak assignment table with a single click, assuming the
constraint is only derived from one peak.

Added the ability to merge constraint lists, and also split constraint
lists, according to ambiguous or unambiguous (pro-chirals don't count as
ambiguous).

Added the ability to display dihedral constaints on the structures.
Increased the number of window navigation options (under the right mouse
menu Navigate), including 3D to 2D and similar.

Added the ability to import constraints, violations and structures from an
Aria2 run directory.

The EditAssignment popup resets scrollbar positions when the peak is
changed. The new resonance button has been created which replaces the
option in the right-hand tables. Added molecule system filtering option.
Correlated dimensions option replaces bound resonances and repeated spin
system options. This new option uses the reference experiment information.
For the peak tables (selected and whole peak list) added a button to put
marks through selected peaks.

Expanded the resonance browser with various navigation and marking
options, similar to Igor Barsukov's macro.

The LinkPeakLists popup now remembers settings (when project is saved). It
also allows you to specify the maximum number of marks to use.

The CopyPeakAssignments popup now uses a distance threshold that is
weighted according to isotope.

Generally, NOE distances do now use r to the -6 averaging.

Can now move the active strip left and right using the buttons at the top
in the strip bar of the graphics window.

Added mouse wheel zooming of spectra, and scrolling of tables.

You can now calculate shift differences for unassigned resonances.

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