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Analysis documentation organisation

Jan 2010 - plans for organising Analysis documentation


Documentation web sites:

We need direct links from the top to 'Analysis Documentation', also to 'Downloads/Installation', 'Report paper referencing Analysis'. The top Analysis Documentation page should have the links to documentation more in focus, and the about/development less.

We need top level links between the in-program documentation (or the on web version of same) and the WIKI. We also need a system for keeping in-parallel documentation for the stable, leading-edge, and likely older versions.

 

High level documentation


Existing Core Concepts

None on Wiki currently. There are Program Highlights, which is good but not the same thing

The Old Release Documentation has a good list, but the entries are too brief.

 

Proposed Core Concepts

  • Experiments and Spectra

    • Experiments

    • Spectra and data files

    • Prototypes

    • Referencing, folding etc.

    • NMR Series
  • Peaks and peak lists

  • Assignments

    • The Resonance – linking everything together

    • Assigning to Atoms – ambiguous assignments

    • Shifts and other measurements

    • Assigning peak dimensions

    • Sequential assignment and spin systems

  • Molecules – templates, sequences, links, and molecular systems

  • Data Analyses: following shifts, relaxation rates
  • Structures and ensembles

  • Restraints

  • CCPN Data Model

  • The Analysis Program

    • Code organisation

    • Spectrum Windows

    • User Interface components
    • Python macros NEW: To include argServer
  • Releases, patches, and data upgrades

 

Existing FAQs:

On Wiki:

Installation:

1 Should I use precompiled versions of Analysis or try to compile the software from source code?

2 Is it possible to run different versions of Analysis in parallel?

3 Which Python versions are compatible with Analysis?

4 Analysis version 2.0 reports python warnings on startup. What does this mean?

5 Can I copy/move an Analysis project from one platform to another without problems, e.g. from Windows to UNIX?

Functionality:

1 Which versions of Aria and Analysis are compatible?

2 How can I export data from an Analysis project, for example a chemical shift list?

3 Is it possible to extract 1D slices from a 2D spectrum and to display them?

4 Is it possible to automate repetitive tasks?

5 Is there a way of recording commands for storage in a macro?

6 How can I transpose or change the axes in a multidimensional spectrum?

7 How can I pick negative peaks?

8 I have recorded a spectrum with a large sweep width, but can only see part of it in the Analysis spectrum window. How can I display the full spectrum?

9 What are regular expressions and how do I use them when filtering tables?

Upgrading:

1 Is there a need to upgrade from Analysis version 1 to version 2?

2 How can I migrate projects from Analysis version 1 to version 2?

Running:

1 Q: Why is OSX complaining that it cannot connect to the display?

2 Q: Why is OSX complaining about the $DISPLAY environment variable?

3 Q: Why is the text of the menus coming out as unreadable gibberish?
4 Q: What do I do if Analysis will not start up because of a coding error?
5 Q: What can I do to speed Analysis up?

 

On old Web Site:

How to pick peaks in a 3D spectrum
How to get help
How to move data from one project to another (NB should be merged with Installation-5 above)

Proposed new  FAQs:

  • I cannot get the installation to work for Analysis / Extend-NMR / FormatConverter
  • Why do I see my spectra twice – why are there 'ghost peaks'
  • My sequential assignments are doing funny things – how can I get back to a clean slate?
  • Why can I not assign PeakDim Xxx to Atom Yyy.
  • Why does an Hbb assignment change to Hba
  • Why does Hd2* show up as bound to Cd1 and vice versa?
  • How can I change my molecule/sequence without losing the work already done on it?
  • Common Error Messages and warnings:
    • Cannot read files, retrying, has project moved
    • Cannot downgrade to older version
    • Project Not Valid, cannot load
    • 'Key already in use' (Same TopObject is several files).
    • Fitting Error
    • Tcl/OpenGL errors


And anything else that results from a review of the JISC mailing list archives...

Following (at least) need updating:

  • What can I do to speed Analysis up.
  • Upgrading and downgrading of data


Existing HowTos


Proposed New HowTos:

  • Create complex molecules
  • unusual amino acids
  • Duplex DNA
  • dimers and polymers
  • Sugars and other non-linear polymers
  • 'Organic chemistry' molecules
  • 'Extra' links: Disulfides, metal complexes, bound ligands
  • Find or create residue templates (ChemComps)
  • Customize Analysis
    • setting up for white/black background
    • Color spectrum series
    • Color by experiment type
    • Fonts
    • Peak Annotations
  • Write your own macros
  • Import data (FormatConverter, special imports, Open Spectrum)
  • Export data (FormatConverter, table export, special exports)
  • Run other programs (Extend-NMR interface)
  • Check for assignment errors, and fix those you find.
  • Find matching peaks
  • Navigate to window positions
  • Assign macromolecular spectra
    • Manually
    • Semi-automatically
    • Automatically
  • Assign NOEs and individual peaks
  • Copy peaks between spectra
  • Make synthetic peak lists
  • Transfer assignments between Experiments
  • Transfer assignments between molecular chains
  • Generate restraint lists
  • Run structure generation programs
  • Analyse restraints and violations for a generated structure
  • Calculate relaxation constants
  • Measure heteronuclear NOEs.
  • Transfer assignments and compare frequencies when peaks have moved.

 

Screencasts

  • HowTos should be done as both text and screencast.