Popup reference

This page lists all the popups currently in use in Analysis. A basic explanation of popups is given in the Popup basics page.

Please report or add any missing links and delete broken links.

Note: The structure of the documentation is largely generated automatically from the core code of Analysis. In some instances this leads to headings that do not reflect the look of the popup itself. We apologise for the possible confusion this might cause in these instances, which are currently being tracked and will be used for further optimisation in a next version of Analysis and its documentation.

Menu structure listing

This list contains all the popups that are activated from Analysis menus and is subdivided into the top menu, window menu and other menu items. Only those menu items that have an associated popup are listed. Descriptions of menu items that are not listed here, can be found in the Menu reference, of which the links are included below.

Note: Multiple different menu items may refer to one and the same popup.

Top Menu

• • Project

  • New

  • Open

  • Close

  • Save

  • Save as

  • Validate

  • User Profile

  • Backup

  • Quit

  • Updates

  • Experiments

  • Open Spectra

  • Edit Spectra

  • Edit Experiments

  • NMR Series

  • Experiment Prototypes

  • Windows

  • New Window

  • Edit Windows

  • Axes

  • Marks and Rulers

  • Print Window

  • Peaks

  • Selected Peaks

  • Peak Lists

  • Draw Parameters

  • Peak Finding

  • Molecules

  • Atom Browser

  • Molecule Setup

  • Add Sequence

  • Residue Information

  • Isotopomer Schemes

  • Assignment

  • Assignment Panel

  • Copy Assignments

  • Quality Reports

  • Initialise Roots

  • Link Peak Lists

  • Link Sequential Spin Systems

  • Link NOEs

  • Automated Backbone Sequence

  • Resonance

  • Resonance Table

  • Spin Systems

  • Spin System Types

  • Reference Chemical Shifts

  • Data Analysis

  • Measurement Lists

  • Rates Analysis

  • Shift Differences

  • Follow Shift Changes

  • 3J H-Ha Coupling

  • Heteronuclear NOE

  • Structure

  • Make Distance Restraints

  • Restraints and Violations

  • Structure Viewer

  • Structure Ensembles

  • DANGLE: Predict Dihedrals

  • CING: Validate Structures

  • Charts

  • Assignment Graph

  • Chemical Shifts Table

  • Secondary Structure Chart

  • Residue Interaction Matrix

  • Ramachandran Plot

  • Macros

  • Organise Macros

  • Other

  • General Options

  • Colour Schemes

  • FormatConverter

    • CLOUDS

    • Resonance Disambiguation

    • Relaxation Matrix Optimisation

    • Proton Molecular Dynamics

    • Filter Clouds

    • Cloud Threading

    • Cloud Homologue Assign

Window menus

• • Assign

  • Assign

  • Predict Spin System Type

  • Deassign selected peaks

  • Clear all sequential links

  • Peak

  • Selected Peaks...

  • Delete selected peaks

  • Find close peaks

    • Find symmetry related check link

  • Match peaks

  • Set details

  • Show structure connections

  • Unalias peak

  • Re-reference to this peak

  • View

    • Contour levels

    • General...

  • Window properties

  • Navigate

  • Strip

  • Markers

  • Options

  • Window

    • Print

  • Macros

Other menus

• • Table menu

  • Filter

  • Export

  • Graph

  • Print

  • Columns Graph menu

  • Set title

  • Print to file

Alphabetical listing

Below is a complete list of popups in alphabetical order, with their full names. The names differ in most cases from the menu items that they are associated with. Documentation has been written for those indicated with an '*'. Popups that cannot be documented because they are not working are indicated with *.

• • Add peak *

  • Add existing contour file *

  • Assignment: Assignment Panel *

  • Assignment: Automated Backbone Sequence *

  • Assignment: Copy Assignments *

  • Assignment: Initialise Roots *

  • Assignment: Link NOEs *

  • Assignment: Link Peak Lists *

  • Assignment: Link Sequential Spin Systems *

  • Assignment: Quality Reports *

  • Backup changed *

  • Browse files * Kept for the moment

• BACUS Control Module

  • CcpNmr Software Updates *

  • Charts: Assignment Graph *

  • Charts: Chemical Shifts Table *

  • Charts: Ramachandran Plot *

  • Charts: Residue Interaction Matrix *

  • Charts: Secondary Structure Chart *

• Cloud Threader

  • Columns Graph *

  • Confirm *

  • Create axis unit *

  • Create axis type *

  • Create new panel type *

  • Create spectrum contour file *

• CING Setup

• DANGLE

• Data Analysis: 3J H-Ha Coupling

• Data Analysis: Follow Shift Changes

• Data Analysis: Heteronuclear NOE

  • Data Analysis: Measurement Lists *

• Data Analysis: Rates Analysis

• Data Analysis: Shift Differences

• Delete Object

  • Dimension number *

  • Directory does not exist *

• Edit Analysis Profiles

  • Edit peak *

  • Edit Peak Aliasing *

  • Edit Project Spectrum and Data Paths *

  • Edit spectrum contour levels *

  • Edit spectrum contour files *

  • Experiments: Edit Experiments *

  • Experiments: NMR Series *

  • Experiments: Edit Spectra *

• Experiments: Experiment Prototypes

  • Experiments: Open Spectra *

  • Export PDB file *

  • Failure * Kept for the moment

• Filter Clouds

  • Filter Options * Kept for the moment

  • generalData changed *

  • Highest scoring mappings *

• Hydrogen Cloud Molecular Dynamics

  • Input text *

  • Import CSI file *

  • Import PDB file *

  • Molecules: Atom Browser *

  • Molecules: Isotopomer Schemes *

  • Molecules: Molecule Setup * Kept for the moment

  • Molecules: Residue Information *

  • New directory *

  • Peak Details *

  • Peak Groups *

  • Peaks: Draw Parameters *

  • Peaks: Peak Finding *

  • Peaks: Peak Lists *

  • Peaks: Selected Peaks *

  • Print canvas to file *

  • Print Structure *

  • Project moved *

  • Project valid *

  • Project: Backup *

  • Project: Close *

  • Project: New *

  • Project: Open *

  • Project: Save as *

  • Project: Validate *

  • Quit CcpNmr Analysis *

  • refData changed * Kept for the moment

  • Read sequence file *

• Reference By Peak

• Relaxation Matrix Optimisation

  • Resonance: Reference Chemical Shifts *

  • Resonance: Resonance Table *

  • Resonance: Spin System Types *

  • Resonance: Spin Systems *

  • Save project *

  • Save table as plain text *

  • Set spectrum referencing *

  • Spin System Type Scores *

• Structure: Make Distance Restraints

• Structure: Restraints and Violations

  • Structure: Structure Ensembles *

  • Structure: Structure Viewer *

  • Text Entry *

  • Update file details *

• Verify Spectra

  • Warning *

  • Window * Kept for the moment

  • Window group name *

  • Windows: Axes *

  • Windows: Edit Windows *

  • Windows: Marks and Rulers *

  • Windows: New Window *

  • Windows: Print Window *