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Beta5 downloads

Downloads for the beta5 release of Analysis Assign, April 2019

Notes on beta5

This is the latest beta release of AnalysisAssign, and the latest update from the beta2 version.  As such, expect there to be bugs.  Please inform us of any issues or feature requests, either by email (ccpn-dev@ccpn.ac.uk) or via the Jiscmail list:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPNMR

Known feature requests and bugs are listed here:

https://bitbucket.org/ccpnmr/issue-tracker/issues?status=new&status=open

Latest Features in beta5

There have been numerous updates to the first beta release of AnalysisAssign, and further updates and bug fixes from the beta2 version; the most important of these are listed below:

  • Updated Spectrum Displays:
    • Improved GL display with new colour schemes offering better contrast of colours; colours can also be user selected
    • New peak symbols, including outline and filled linewidths
    • Reduced cluttering of information
    • Locking of axes aspect ratios
    • Axes can be displayed as ppm, point or Hz
    • New zoom preferences
    • New grouping of peaks into Multiplets
    • Integral regions new to 1D spectra
    • Exporting high quality images from spectrumDisplays or individual strips in pdf or svg format
    • Strips displayed in a scroll area with resize options
    • New phasing console allows visualisation of phasing traces across different planes
  • Updates to Gui Modules:
    • Improved Tables: speed improvements and new advanced search option and columns filter, added exporters to CSV/TSV/Json/xls/ for all tables
    • Improved speed for module updates
    • Quicker assignment routines, including editing and deleting
    • Improved undo features
    • Drag and drops for quick assignments from sidebar
    • New functionalities on Chemical shift mapping module
    • Macro editor with Python Syntax
    • Plugin mechanism available
    • Saving and restoring Layout, current, strips
    • Module right click options
    • More drag and drop options from the side bar; drop area accepts mostly all CcpNmr objects
    • Redesign of modules and popups, in particular
      • NmrTable
      • Preferences
      • SpectrumProperties
      • PeakAssigner
      • Improved Assignment Inspector Module
      • Chemical Shift Mapping includes interactive bar Chart and pymol integration
    • More Gui features
    • Copy PeakList across spectra: Via Popup or Drag and drop of PeakLists from SideBar.
      • Drag and drop NmrResidues on SpectrumDisplay
  • More mouse commands:
    • move peak
    • snap peaks to extremum
    • select all peaks
    • move to next/previous spectrum
    • More actions from tables.
      • Double-clicking peak table entry zoom/moves current display to peak location
      • Double-clicking nmrResidue table entry zoom/moves current display to nmrResidue location
    • More right-click context menues
      • context sensitive options for peaks
      • options for phasing
  • Tutorial's and How-To's:
    • Beginner (new simplified version)
    • Backbone Assignment (new simplified version)
    • CSP tutorial
    • New How-To's for Sparky, Nef, and screening

There have also been many bug fixes and improvements to the undo/redo features.

Licence and Updates

To get an updated licence download for beta5 users whose licence has expired, fetch the following .tgz or .zip file and unpack it inside the top-level directory of the release from a terminal.

The licence below is valid until 28 May 2019.

http://www.ccpn.ac.uk/download/b5/Licence.tgz

tar xzf Licence.tgz ~/home/user/projects/Analysis

or alternatively use unzip:

http://www.ccpn.ac.uk/download/b5/Licence.zip

unzip Licence.zip ~/home/user/projects/Analysis

The licence can also be updated from the terminal by running bin/update or from the Check for Updates... option from the Help menu.

Mac download

The Mac download was compiled on OS X 10.10.5 (Yosemite).  It consists of a zip file.  When you have downloaded this, just unzip it where you want on your disk (except no blank spaces in the directory path).

There are three options for running the program:

  • In the top level of your Analysis folder, double-click the .app applications
  • Open up an ordinary Mac terminal window and run open ./AnalysisAssign.app which will run the .app as if you had double-clicked
  • Open up an ordinary Mac terminal window and run bin/assign.  You can add the bin/ directory to your PATH, in which case you will then be able to run it just by typing assign. (Creating a symbolic link to assign will not work)

On the first running of the .app you may experience issues with the MacOS routine quarantining of downloads, if this happens, please following the instructions in the popup.

Download the MacOS version from here:

http://www.ccpn.ac.uk/download/b5/ccpnmr3.0.b5MacOS.zip

tar xzf ccpnmr3.0.b5MacOS.tgz ~/home/user/projects

(Currently contains a licence until 28th May 2019)

The MacOS download does not contain the following example data files and tutorial projects.

Data and Examples

The following download contains tutorials and examples to experiment with. Download to your downloads folder and then extract to your projects folder, e.g. ~/home/user/projects, which will give you a new /data subdirectory:

http://www.ccpn.ac.uk/download/b5/data3.0.b5.tgz

tar xzf data3.0.b5.tgz ~/home/user/projects/Analysis

or alternatively use unzip:

http://www.ccpn.ac.uk/download/b5/data3.0.b5.zip

unzip data3.0.b5.zip ~/home/user/projects/Analysis

Linux download

For Linux, the current distribution is Lubuntu 18, download the following and extract it:

http://www.ccpn.ac.uk/download/b5/ccpnmr3.0.b5Linux.tgz

e.g.: tar xzf ccpnmr3.0.b5Linux.tgz ~/home/users/projects

(Currently contains a licence until 28th May 2019)

This might also work for some other flavours of Linux (please let us know if they do!). If they do not work for a particular Linux variant, please contact us to see if we can work with you to get a distribution ready.

Virtual Machine download (including data)

Whatever your operating system, you can run the CcpNmr programs from a virtual machine. First you must make sure you have VirtualBox program and the VirtualBox Extension pack - you can get it for free from:

https://www.virtualbox.org/wiki/Downloads

You then download the AnalysisAssign VM (with data), extract it, and open it with VirtualBox:

http://www.ccpn.ac.uk/download/b5/ccpnmr3.0.b5VM.zip

e.g.: unzip ccpnmr3.0.b5VM.zip ~/home/Users/Projects

The VM runs Lubuntu, a light flavour of Linux and includes the fully working program with all tutorials and test data.

General comments

As soon as you start up AnalysisAssign, the first thing you should do is get the updates.  These can be obtained via the help menu: Help --> Check for Updates. Once you have installed the updates, you need to quit the programme and restart it in order for the changes to take effect. If no updates are available then it will show a count of 0.

Notes for Analysis v2 users

If you open up an Analysis v2 project in v3 then it will automatically get converted to v3 format. The main difference between the formats for v2 and v3 is that in v3 the top-level directory has a ".ccpn" suffix attached, and the xml files are one level further down, in the sub-directory ccpnv3 of the project directory (inside that sub-directory you will find memops/, ccp/ and ccpnmr/, as usual).