The Example described here is ex_1 from the teaching examples which are in the folder \xlearn.

Start Oscail click the button, set Files of type to All files and navigate to the ex_1 example in \shelx\xlearn.

select either of the ex_1 files and click Open.

The correct Jobname and Current Directory should be on the status bar.

The first task is to determine Z (the number of molecules in the unit cell, the crystal system and the space group. Select Edit / Edit.TXT.

Z is estimated using the approximation that each non-H atom occupies 20ų.
Thus Z = 1638.9 / (20 x 20) = 4 and the crystal system is orthorhombic.
Close the editor window. Absen is used to help with space group choice. Click and select Absen and Run

Select Space Gr.from Abs. on the menu and select Orthorhombic on dialog3 and OK.

The analysis shows the 3 2₁ absences and the space group is uniquely determined to be P2₁2₁2₁ No. 19.
There is now sufficient information to solve the structure using direct methods. Run Genins as you ran Absen (it is on the top left of the dialog).

The defaults are all suitable click OK and OK on the comment entry dialog.

Enter the cell dimensions and click OK

Z is correct so click OK.Click OK to the next dialog and enter the space group name on dialog 3 and OK.

The molecular formula must be entered correctly.

Click OK and the mean volume per non-H atom is computed this should be reasonable and it is a check on the entered data. Click OK on dialog 13 and OK to exit. As suggested in the hints you must use SHELXS-97 select this and Run.

Select Yes on Review Screen Output.

The best CFOM is 0.0934. Click the screen again and Select NO on Review Screen Output.

 Click OK to run Ortex.

Click OK to use the defaults.

There are 20 non-H atoms in the molecule the program suggests that 21 peaks be taken from the MAP. Click OK to accept this and select defaults until the following screen appears.

Follow the instructions and in  ORTEX and run ShelxL. When ShelxLhas finished select NO to Review Screen Output. Follow defaults back to ORTEX and you should have



Two of the atoms are blue because they have thermal paramaters which are larger than a limit set in ORTEX setup. They are rubbish go to edit (Ed) select each of the blue atoms using a left mouse click and delete using d/D. When they are deleted click the right mouse button and click YES to Add Changes and defaults on any other dialog. to update the files.
Run ShelxL again. You should now have

There are now no blue atoms but one atom is missing. This is easily found in the difference map as follows.
Run ShelxL and click No on the Review Screen Output message. Select defaults until the ORTEX options appear.
Check that the Sel. Peaks from MAP or DIFF MAP option is selected and click OK.



Only one peak is required and as this is the default you could use defaults however Check Review Peak List on the next dialog to see the Diff. map peak list.





The first peak is Q1 and it is much larger than Q2. Select defaults until the following screen appears.

 

All of the non-H atoms have been found. To set the atom names click  to show atom labels The only atom correctly labelled is P1. Q2 is O1. In edit select Q2 and press c and set the name to O1. Repeat this for the atom you want to be C1. The rest of the carbons can be renamed using auto incrementing. Select the C2 atom and press n.  Repeat for the other carbons. Click ANIS in edit mode and run ShelxL again. All of the atoms should now be anisotropic and the carbons will be last and sorted in the INS file. The R factor is now 10%. It is essential that atoms are properly numbered before hydrogens are added.

Hydrogen atoms are added one HFIX instruction at a time. Taking the aromatic carbons first click HFIX.
This will bring up the start of the HFIX command.



This is suitable for the aromatic carbons.
Now click the carbon atoms to select them. Press h/H when an atom is selected to add it to the current HFIX.
The selected atoms will have blue labels after they are added to the HFIX. Right click to add the HFIX to the INS file and click Shelxl.
On return to ORTEX you should now have.



The methyl H-atoms can be added using HFIX with the 137 instruction.
When all of the H-atoms have been added click the Printer icon on the toolbar in atom mode and select PNG (2400 x 1800) and OK
If you insert this PNG file into WORD you should get.

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