HowTos

This page lists the HowTos written for Analysis. The HowTos listed here illustrate one of several ways how to perform a specific task in Analysis. The HowTos are categorized similar to the way functionality is organized in CcpNmr Analysis. How to get help with CCPN analysis, FormatConverter and the data model API are found here.

Please feel free to add contributions and make changes where appropriate.

Projects

• Create a new project

Experiments & Spectra

• Load spectra

• Deal with multiplications of spectrum contours

Windows

• Navigate between windows

• Transpose the axes in a multidimensional window

Peaks & Peak Lists

• Add a peak list to a spectrum

• Pick peaks

• Pick and assign 3D peaks from 2D root peaks

• Find matching peaks

• Copy peaks between or within spectra

• Copy assignments between peaks

• Copy assignments between molecular chains

• Make synthetic peak lists

• Transfer assignments and compare frequencies when peaks have moved

• Unaliase a peak

• Separate peaks and estimate peak volumes using the Peak Separator

Molecules

• Create a new molecule from a sequence

• Create disulfide bridges in a molecule

• Set up multimers: dimers and homodimers

• Create duplex DNA

• Create a sequence with unusual amino acids or nucleotides

• Create and import a residue template

• Add a non-standard small molecule

Assignments

• Assign a peak

• Assign NOEs based on structural information

• Assign groups

• Propagate assignments

• Check for assignment errors

• Make an automatic sequential assignment using Nexus

• Run MARS from Analysis

• Predict a spin system type

• Predict the residue type of a spin system and the optimal arrangement of residue types

• Inspect and modify spin systems and resonances

• Get more assignment possibilities

Customize Analysis

• Set contour levels

• Set contour colors

• Set aspect ratio

• Set crosshairs

• Set 1D slice range

• Set keyboard shortcuts

• Set spectrum display options

• Set window names

• Set the window background color

• Set fonts

• Set peak annotations

• Set peak box size

• Arrange peak labels

Structures and Restraints

• Generate restraint lists

• Merge and split restraint lists

• Analyse structures

• Analyse restraints and violations for a generated structure

• Run CING from Analysis

• Run structure calculation programs

Data transfer

• Export data

• Import data

• Move data between projects

• Get updates

Data Analysis

• Calculate T1, T2 or T1rho relaxation constants

• Calculate heteronuclear NOE values 

• Calculate 3J H-Ha coupling constants

Macros

• Write a macro

Installation

• Analysis 2.x on CentOS 5.x with standard libraries

• Analysis 2.x and Aria 2.3 on CentOS 5.x with Python 2.7 & Tcl/Tk 8.5

• Analysis 2.x and Aria 2.3 on CentOS 7.x with standard libraries