Nmr specific options (NMR)

Introduction.


The options can roughly be grouped in four classes:

1) Coupling with Aurelia and UXNMR.

2) Coupling to distance geometry program(s)

3) Application of WHAT IF options to groups of chemically identical but structurally distinct molecules.

4) Other options.

Coupling with aurelia and uxnmr.

These couplings have not yet been made.

Coupling with distance geometry programs

Reading diana output files (GETDIA)

The command GETDIA can be used to read a DIANA output file. You will be prompted for the file name and for the set name.

Multi molecule options

One of the problems with solving structures by NMR is that there are always very many (hopefully very related) structures that fulfill the NOE requirements to the same extend. One therefore has to operate on many molecules at the same time. WHAT IF is especially good in doing so because of the very large number of molecules/residues it can hold in memory.

All multi molecule options expect a list of molecules to work on. The first molecule in this list is the main molecule (for example the one on which to superpose all other ones). The USEMLS option can be used to define the list of molecules.

List of molecules to be used (USEMLS)

The command USEMLS has to be used before any of the other multi-molecule options. With USEMLS you define the list of molecules to be used in subsequent multi-molecule options. Use USEMLS again if you want to change the list of molecules to be used.

The first molecule in the list is the main molecule. Superpositions will be done on this molecule. Comparisons will be made with this molecule. When you are prompted for a residue range, you should only give residues in this molecule, WHAT IF will then automatically determine the equivalent residues in the other molecules.

The list of molecules should at least hold two molecules.

All molecules in the list of molecules should be covalently identical. That means that they should have the same sequence, the same atoms, but are allowed to have completely different structures.

Check the list of molecules (CHKMLS)

The command CHKMLS will cause WHAT IF to move over the list of molecules, and check if they are all covalently identical. If they are not, you can still try to run the multi-molecule options, but a crash might be your reward for that...

Read multiple PDB files (GETMLS)

The command GETMLS can be used to read a series of molecules. It is required the your files adhere to the following naming convention:

All file names start with a non-numerical part.

The middle part of the name is numerical. This numerical part has no leading zeros. The numbers are supposed to be unique, and increasing continuously without ever having more than 9 files in a row missing.

File names end with a non-numerical part.


You will in row be prompted for:

The leading non-numerical part of the names.

The number of the first file.

The number of the last file.

The non-numerical tail of the names.

So for example: you want to read the files:

   MOL2.DG
   MOL3.DG
   MOL4.DG
   MOL5.DG
   MOL7.DG
   MOL11.DG
   MOL12.DG
   MOL13.DG
   MOL15.DG
   MOL19.DG

Then you type:

   MOL
   2
   19
   .DG

Be aware that if in between files (eg. MOL8.DG) do exist, they will be read...

Superpose multiple molecules (SUPMLS)

The option SUPMLS will first show you a small mini menu. From this menu you can decide to either automatically superpose all molecules on the first one, or define ranges yourself to use for superpositioning.

The automatic superposition will run the MOTIVS option (see chapter on SUPPOS) on the first molecule and the second, the first and the third, etc. All matrices will automatically be applied. So in contrast to MOTIVS in the SUPPOS menu, you do NOT have to use the APPLY option at the end. It is rather likely that the residues used to superpose on are not the same for all molecules.

In case you choose to manually define the residues on which to superpose, you will be prompted for these residues. Here you can give residues in the first molecule of the molecule list defined with the USEMLS option. In all other molecules the equivalent residues will be selected to determine the superposition transformation. The resulting superposition transformation per molecule will be applied to that whole molecule.

Alpha carbon tracing (CAMLS)

The option CAMLS will cause WHAT IF to prompt you for a set of residues in the first molecule that you gave with the USEMLS option. It will than display the alpha carbon traces of all equivalent residues in all activated molecules. The molecules will be colored purple till yellow in the order you typed them in the USEMLS option. The first C-alpha trace will be drawn in green

Displaying a zone of residues (ZONMLS)

The option ZONMLS will cause WHAT IF to prompt you for a set of residues in the first molecule that you gave with the USEMLS option. It will than display all atoms of all equivalent residues in all activated molecules. The zones will be colored purple till yellow in the order you typed them in the USEMLS option. The first zone will be colored by atom type.

Averaging structures (AVRMOL)

The option AVRMOL assumes that all molecules in the soup are proteins that are chemically identical, but have different structures. The option will cause WHAT IF to generate one more molecule in which every atom is placed at the center of gravity of all equivalent atoms in soup. This averaged molecule has of course not proper geometry!

Topology file (TOPOLO)

The command TOPOLO will prompt you for the name of a (new) topology file. This file will than be read and WHAT IF's entire internal administration will be updated. Be aware that the soup will be initialized by this command. Also, many files saved with commands like SAVSOU in the SOUP menu can now no longer be read....

Other options

Display the handedness of residues (NMRHND)

This option will cause WHAT IF to prompt you for a distance cutoff. It will then consider all groups of alpha carbons that fall within this distance of each other, and determine the hand of the two residues that make a contact and send a cross to the graphics screen colored as function of these two hands.

Backbone complete ball and stick model (BBBALL)

The command BBBALL will prompt you for a residue range. It will than draw the backbone for this range as a normal stick model, but with the hydrogens included if requested.

On top of that, small dotted spheres will be added for all atoms. The hydrogens will become orange.