The FormatConverter web interface

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About

The CcpNmr FormatConverter web interface was designed to facilitate conversions between any existing NMR data formats and types. The underlying code is based on the existing CcpNmr FormatConverter code written by Wim Vranken, and was interfaced to this web site in a collaborative effort by the team from the CCPN Project, the EBI in Hinxton, and Spronk NMR Consultancy.

What the web interface does

The FormatConverter web interface aims to facilitate the most common and simple conversions from one format to another. In addition, it can create new or import existing CCPN projects, and makes them available for download at the end of the conversion session.

What the web interface doesn't do

The web interface is not designed to provide all NMR format inter-conversion possibilities. For more complicated conversions and CCPN project manipulations we advice to use the standalone version of the CcpNmr FormatConverter or access it from CcpNmr Analysis. This software has been more extensively tested and provides a higher level of user interaction.

Screencast Tutorial

The CCPN FormatConverter online demonstration by Jurgen Doreleijers (CMBI). Large size here.

How the web interface works

The web interface was designed to guide the user through the format conversion process in a series of simple, intuitive steps on various web pages. The steps are:

Starting a format conversion session from a new or from an existing project
Selection of the input data format
Selection of the input data types
Importing data
Selection of export data format(s)
Selection of export data types(s)
Exporting and downloading data

where the following scheme describes the pathways between the different pages:

Before starting

Using the CCPN data model virtually any conversion is possible, with a large variety of input and output conversion options. With this versatility comes complexity and sensitivity to erroneous input. Even though great effort was put into optimising user feedback, error messages and automated parameter settings, it is of great importance that correct and compatible input is provided in order to reach a satisfactory result. So before proceeding, please check carefully the consistency and compatibility of your input files. It is recommended to keep individual conversion sessions as simple as possible.

Starting a format conversion session

Since the FormatConverter code is based on the CCPN data model, all format conversions require CCPN projects as an intermediate. CCPN projects are either created or uploaded at the start of a conversion session using the

and

buttons.

Starting a session from scratch: "New project"

A session using a new project is used mainly for all non-CCPN to non-CCPN format conversions, e.g.:

Xeasy to nmrView
CNS to Cyana
etcetera

But can also be used to create a new CCPN project from non-CCPN data, e.g. in case when it is desired to port data for use in CcpNnmr Analysis.

Creating a new CCPN project

Starting a session using an existing CCPN project: "Load project"

A session using an existing project can be used to:

convert data from the CCPN project to other formats
import new data into the CCPN project

Loading an existing CCPN project

Selection of the input data format

The selection of the input data format is done from a drop down list that lists all the supported NMR formats. The input format selection page can be accessed when:

when a new project is initiated
after upload of an existing project and selection of the option to import data
after selection of the option to import more data

Selecting the input data format from a drop down list

Selection of the input data types

Selection of input data types always follows the selection of the input data format. A list of data types available for the corresponding data format is shown. In some cases pre selections are made of data types that are normally considered necessary for interpretation of the data.

Selecting various data types for the input format

Importing data

Importing of data is the most complicated step in the format conversion procedure.

Selecting a file for upload

Click on the "Browse" button to select a sequence file to import. Then, press the "Upload and validate" button to upload the file. If the file is not in the correct format (in this case, the file should be an Xeasy sequence file), then the FormatConvert web browser will give you a message and advise you to select another file. If you have not selected a file, you will also be given a message to select one. You can also avoid this step by pressing the "Don't import" button, and in this example, you will move onto the import of chemical shift files.

An uploaded and validated file

[Question: what if molecule is not a protein?]

Once you have successfully uploaded a file, there will be two new buttons at the bottom of this table called "Show more" and "Import". If you click on the "Show more" button, you will receive more options as shown below. If you have a fairly straightforward sequence, you can choose to import your file into your CCPN project using the "Import" button at the bottom of the sequence import table.

Display of advanced options from the "Show more" button

If you "mouse" over the field titles on the left of this advanced option table, then you will receive some extra help in a popup text field. The options on the right side of the table contains places for you to change the options as text/numeric fields, radio buttons or pulldown menus. You can hide this table at any point using the "Show less" button at the top of this table.

You can automatically link your sequence (what does this do?). Your molecule may be a homodimer, in which case you need to write "2" in the "Number identical chains" field. You can also ignore chains that only have one residue in them (in the box called: "Ignore single residue chains") or that have residues that are unusual chemical components ("Ignore unknown chemComps").

If you project already has a molecular system in it (which may be an empty one), you can import your sequence into that one. Choose from the pulldown menu in the "Use existing molecular system" box. This is actually a more advanced option and you will probably always want to create a new molecular system, and is more useful if you find that your sequence has slightly changed due to a change in how you clone your sequence. If the part of your sequence that you are studying is only a subset and the sequence of the complete protein (or other polymer) is longer, you can enter the position in that polymer sequence that you have in your experimental molecule in the "Sequence code start" text field.

Finally you can call the molecule something more meaningful in the "Molecule name" field, otherwise your molecule will get a default name. Once you have selected all the options, then you can import your sequence using the "Import" button. at the top of the advanced options menu. If your sequence imports correctly, then you will be advised about this by some cyana-coloured text with something like "Imported file:NapD.seq" on the right side of sequence import table.

Now, click on the "Done" button at the bottom of this table, and a new table will open up below for you to import another file - in this example, it will be a table to import an xeasy chemical shifts file.

All files have been imported and processing options are displayed

Once you have imported all your files, your web page will look something like the above screenshot.

Selection of export data format(s)

Based on the data that are in the CCPN project, a list of possible export formats and data types is created internally. The list of exportable data formats is given as a multi selection list, from which any combination of data formats can be selected.

Multiple export data formats can be selected at once

Selection of export data types(s)

Selection of export data types always follows the selection of the export data formats. For each selected export format, a multi selection list is presented of all possible data types. After selection, the "Next" button will take you to the download page.

Multiple export data types can be selected for all export formats

Downloading data

After the converted data have been exported they are listed as downloadable files on the download page:

Individual files can be downloaded from the list of links to the respective files.
A complete file tar/gzip file archive can be downloaded using the "Download all" button
The CCPN project can be downloaded using the "Download CCPN Project" as a tar/gzip file archive

The CCPN project file and individual exported files can be downloaded or all at once

Known issues

Django development server is known to crash occasionally without reporting an error on apple Mac and some linux systems.

Subpages (1): Exporting from existing CCPN project

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