Welcome to NMR Constraints Analyser

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with X-Ray crystallography, a major technique for determining high resolution three-dimensional structure of macromolecules. The output of an NMR experiment includes a set of lower and upper limits for the distances between pairs of atoms (constraints). If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the protein satisfying the data. The more constraints are measured, the better defined these structures will be.

Thus here we provide with a tool aimed at analysing the distribution of NMR constraints per residue.

  1. Input
  2. Output
  3. Actions
  4. Supported Formats
  5. Contact us

Input

input The program has several input options:
  1. Insert a PDB entry id and look if corrispondent NMR data is available in BioMagResBank NGR-FRED&DOCR database. This option is recommended because we ensure an automatic upload and maximun compatibility.

    Otherwise you can:

  2. Insert

    i) The .mr file containing the constraints obtained from an NMR spectroscopy experiment that can be downloaded from the RCSB PDB databank. Currently we support two formats frequently used, i.e. Cyana/DYANA and XPLOR/CNS (For more information go to the Supported Formats section).

    ii) The .pdb file, containing the three-dimensional coordinates of the molecule's atoms divided per model.

Note: in the case of multi-chain pdb files, we recommend to first try the search through the NGR-DOCR database, or choose the format XPLOR/CNS. Furthermore, the user can choose among the chains and which of the NMR's PDB model to use.

For a simple TRYOUT select one of the examples and click "Visualise constraints"

Output

Upon calculation completion, the user will be directed to the following page: mini

Header section

Initial

The header section gives general information about inserted macromolecule. Additionally there is the possibility to change the analysed chain (if more than one chain is present) and to visualise constraint types' distribution in a pie chart clicking onto the highlited link. Pie popup

Graph&Jmol section

Graph and Jmol

A clickable bar chart graph shows the distribution of constraints per residue together with information about violation and completeness (as reported in BMRB's FRED database, more details about completeness can be found here) In addition a Jmol applet visualises the structure of the analysed macromolecule coloured according to the constraints distribution.

This was possible by overwriting the 11th column of the pdb file, which for X-ray spectroscopy contains the beta-factor, with the amount of constraints per residue.(Example below) We offer to download this modified file by clicking on the Pdb file name in the header section.

modification

Actions

You can choose to visualise a residue in detail, to do this, click on the green/white (according to presence of torsional constraints) dots in the graph or select it in the field below. The model viewer(JMOL) will add the residue structure and centre the visualisation and on it. Also the second select menu will now list all the atoms of the residue which were found to be involved in a constraint.

select action

To visualise the constraints on a particular atom, select the name in the menu and click view. A table table will be generated below showing all the constraints atom per atom.

select2

Moreover you can decide to visualise a constraint in Jmol. In order to do this simply check the checkbox in the last column. By zooming in Jmol (Scroll muose) you can better appreciate the location of the constraint.

select2

You can add as many tables as you want as well as delete them or by selecting "view all" generate tables for all atoms of selected residue. Also in Jmol you have the possibility to reset the visualisation of the aminoacids by clicking the remove button, whereas to reset orientation simply click reset. Moreover all Jmol features can be used trough its menu, accessible by a mouse-right-click on the JMOL window. If you want to know more about Jmol or find many tutorials visit the Jmol-website

Supported Formats

The supported formats are:

A working multi-chain file in CNS format should look like this: CNS MULTI-CHAIN

For file format conversion refer to BMRB data bank

Contact us:

Developed by Davide Martin Heller and Dr. Alejandro Giorgetti
for support,comments or suggestions mailto:

davidemartin|heller*univr|it <== Replace | with . and * with @ to have the right email address. or alejandro|giorgetti*univr|it <== Replace | with . and * with @ to have the right email address.


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