A worldwide e-Infrastructure for NMR and structural biology

Getting Started with CcpNmr Analysis

If you’ve not used CcpNmr Analysis before you may want to know what it’s all about, so here are some highlights of the software.

Spectrum Windows

An Analysis project may contain an almost limitless number of spectrum windows. The windows are are inherently N-dimensional with scrollbars for not only the screen dimensions but also for orthogonal planes, with the ability to select any plane thickness. A window can be divided into several strips for easy comparison of different regions of spectra. Many spectra may be superimposed in the same window where their contours and peaks are readily toggled on or off. Navigation is achieved by using the mouse or keyboard and there are inbuilt navigation functions to easily find orthogonal planes and return-peak positions etc. Many functions may be applied to crosspeaks directly from the window menu. For example peaks may be assigned, deleted, unaliased and shift matched. Several of these functions can be used on several peaks at once to improve user efficiency. For example, columns of NOE peaks derived from the same amide resonances may be assigned to this amide at the same time.

Molecules

Polymer chains and small molecules are readily put into NMR projects. Sequences may be imported from file or entered directly by the user and from this Analysis will build the molecules with all of their NMR assignable atoms. Many molecules of different types can be included and may be connected together into chains. For example, a GIP-anchored glycoprotein may be constructed by joining protein, sugar and lipid components. By using data provided by the PDBe group at the EBI, CcpNmr software has access to a large number small molecule templates - those that have appeared in PDB structures.

Tables

Virtually all of the information within a project is available to the user via a graphical interface (and a Python shell should you be brave enough to use it) and much of the commonly used information is presented in tabular form. These tables are used to display peak lists, chemical shifts, constraints, coordinates, spectrum configuration and the like. To allow the user to change information (peak position, contour colour, experiment name to name only a few...) they often have editable columns. The rows of the table may be sorted on any of the column types, may be filtered according to a search expression and may be selected (often several at once) to apply specific functions. Also, the data in a table may be exported to a text file, output as PostScript and if numerical may be plotted in a graph.

Resonance Assignment

Assignment in CcpNmr software is a two-step process proceeding via an intermediate Resonance object. This allows the user to represent anonymous but connected assignment states, and allows atomic assignment to be made to several peaks at once. Most crosspeak assignment is made by the user choosing a resonance (which need not be assigned to specific atoms) from a curated/ranked list. The choice is made with a single click (and is readily reversible) from a list of possibilities that are close in chemical shift. Structural information can also be used in assignment. Here through-space linked resonances may be ranked according to their distance in an intermediate structure.

Assignment of resonances to specific atoms is achieved by selecting the atom on a display showing the well-curated molecular information. This needs to be done only once for each resonance as all peaks which correspond to the same resonance will automatically share the atom information. A resonance may be assigned, where appropriate, in a stereospecific or non-stereospecific manner. For example, it is possible to say that two peaks represent two different hydrogen beta atoms in a residue, with different chemical shifts, but without necessarily specifying the stereochemical arrangement of the two atoms.

There are many tools designed to expedite the resonance assignment process, including using root resonance locations (e.g. amide) to direct peak picking and assignment in higher dimensionality spectra, automated matching of peak positions for sequential protein backbone assignment and chemical shift plus structure based filtering of NOE/through-space assignment possibilities.

Structure Generation

Analysis can be used to generate distance and dihedral angle restraints for structure generation. Distance restraints may be generated from assigned NOESY peaks, or may be created by performing shift matching on unassigned peaks. The potentially ambiguous constraints thus output may then be used by programs, such as ARIA, which are able to take input data from a CCPN project and write the results back. The violations that result from a structure generation cycle may be imported into Analysis, from where the user can readily follow a link to the peaks which were used in the generation of the violated constraint. Connections to the CING software allow easy validation of macromolecular structures.

Data Analyses

Analysis has specialist tools to extract relaxation rates, chemical shift changes, kinetic parameters, scalar couplings etc. These are designed to make such tasks in NMR less tedious, and the program aims to automate as much of the simple parts of the processes as possible. For example when following chemical shift changes in titration experiments Analysis automatically tracks the trajectories of shifting peaks so that the titration points can be considered as an analytic group. The program also goes on to fit equation curves to the data and extrct the relevant paremeters.

Reference information

All the CcpNmr programs have access to a library of reference information. This includes chemical compound descriptions, chemical shift distributions, isotope information, idealised residue coordinates etc. This is often used implicitly within Analysis, so that the user doesn’t have to worry about how to get hold of such information. Some of the data is visualised where it can be helpful. For example, chemical shift distributions during assignment.

Practical matters

To get started with CcpNmr Analysis you must first download the latest stable version of CcpNmr Analysis at http://www.ccpn.ac.uk/downloads/stable as a pre-compiled TGZ archive and agree to the full details of the CCPN license. For a Linux or Mac release you just need to unpack the file (e.g. issue the command "tar xvzf analysis2.1.5.tgz") and for the Windows release just double click on the CcpnmrSetup-build-2.1.5.exe file. To start Analysis on Linux or Mac make sure that the extracted bin/ directory is on your executable path (e.g. set $PATH in your .bashrc or .cshrc file) or run bin/analysis directly. To run Analysis from Windows double click on the icon.

Next try the beginners tutorial at http://www.ccpn.ac.uk/software/tutorials/analysis-beginners/beginners-analysis-1.

Documentation

The documentation for CCPN software and programming within the CCPN system is divided into several sections. The main high-level documentation with tutorials, frequently asked questions and how-tos are housed at the CCPN Wiki site which has mainly been done in a collaboration between CCPN and Spronk NMR Consultancy, although there are a few tutorials on the main CCPN site. The low-level, detailed documentation about all of the individual popups and graphical elements in CcpNmr Analysis and CcpNmr ChemBuild can be found at the site for in-program documentation, which is largely generated from tool-tips and documentation strings embedded in the Python code (it is nonetheless proper English). For programmers who wish to develop software using the APIs to the CCPN data model, for example to write macro scripts for Analysis, there is the main Python API and data model documentation and also a short API programming tutorial script to help get started.

 

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life