Tutorial
Sucrose 5

Type 'reset'  and then 'solve'. We now have Q peaks on the screen again. For demonstration purposes, we are going to delete these atoms. There are two ways of doing this:

Press the <DEL> key
Type 'kill sel'

 

Note:

         The keyword 'sel' is used very often in OLEX. It always refers to the current selection, ie the highlighted atoms on the screen. Next, type 'sel $H' - this will select all hydrogen atoms in the structure. Delete the entire selection.

 

Proceed if the screen is clear.

 

In this section, hydrogens will be put back into the model and the the atoms will be renamed. These steps can be done in any order. The 'Naming' panel can be found under the tab 'View'

Click on the 'Mode' button in the naming panel, and then click on the atoms in the order you want them named. Once you are done, either press the 'Done' button or hit the ESC key to get out of this (or any other) mode. The 'Sel' button will do the same thing, but using a already selected selection of atoms.

Using the concept of the mode, you can now geometrically place all hydrogens in their appropiate mode. Click on the small dots on the left hand side of the panel to expand the options.

Now refine the structure.

Proceed if your structure has refined and all hydrogens are back

 

 

 

 

 

You will now refine this model. One of the itmes available to you when the tab 'WORK' is selected above, is this 'Model' panel, reproduced below. You can now click on 'Refine' to refine your modified structure.

Click on both of the red bars representing the q-peaks (open the panel Q-Peaks if you can't see them) to select the two highest peaks. Then type 'name sel O' to change the Q-peaks to oxygen atoms. Alternatively, right-click on the Q-peak you want to change and select the atom type from the list.

Type (or click) 'refine'. The two oxygen have now been refined isotropicaly. Select them both, and type anis sel or else click on the appropiate link in the 'Model' panel above. Then refine again. You might want to adjust the numbers of L.S. cycles you want and the numbner of Q-Peaks you wish to see by typing 'refine 4 10'

Proceed if you have the two previously deleted oxygen atoms back