Water fitting

(10 minutes)

Introduction

When you start the tutorial, there will be a few seconds' delay. This is because the program must generate a sphere of symmetry atoms, and then make sure the map covers these atoms. The message line at the bottom of the graphics screen will indicate the progress of the setting up. The water palette will appear with only 4 tools that can be selected.

The graphics display will show the molecule of insulin, the ligand, and a blue sphere of symmetry atoms.

Before you begin

To complete this tutorial you need a licensed copy of QUANTA that includes either of these modules:

• X-BUILD
• X-AUTOFIT

Starting up the tutorial

This example requires the file water.tar.Z. <Shift>-Click on it to copy it to your area. Then click OK in the next window that comes up. Make a note of the directory into which the file is going to be saved.

Now cd to that directory. Uncompress and untar the file by typing:

uncompress water.tar.Z
tar xvof water.tar

Now type:

cd water

And start QUANTA:

quanta

When QUANTA has finished loading, select Applications / X-SOLVATE. This starts the water fitting tutorial.

1.) Finding possible sites for waters

Click the palette tool Search for waters. This searches the map within the displayed sphere for possible sites for waters, and sorts these in order of peak height. This takes approximately 2 - 3 seconds. The display centers at the first (largest) possible ligand site, the map appears (contoured at 1 and 2 sigma), and a theoretical water site is indicated by a rhombohedral cursor, including non-bonds (yellow) and hydrogen bonds (white).

You can move the water site using the dials. The water would move more quickly with the map off, but this would prevent you from finding the best position for the water. For a single spherical water site the program will normally find the best position (by quadratic interpolation) without any need to move the site position.

You can tell the program that this is a water site using the Save as water tool. A red cross then appears at the pointer position.

Now go to the next site with the Next peak tool, and save this as a water.

You can continue for all the water sites, saving each probable site as you go.

2.) Saving the results

Picking the Exit tool saves the new water position as a new file, while the Quit option leaves and make no changes.

3.) Other things to try

Click the Change search setting... tool.

You can investigate changing various parameters as you wish.

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