To manually focus the telescope first turn the automatic focus finder off by clicking on the "none" button in the Hexapod gui.

Then go back to the Observer Console gui, click on the Exposure Control tab, and start the focus procedure by selecting "focus" from the exposure type selection.

Choose an exposure time of 5-15 seconds and your desired filter (for example, r).  Choose a shift of 30 rows, your desired number of focus steps and your desired focus step size.  An image will be taken of N expsosures (number of focus steps specified), stepping the focus and shifting the charge by a number of rows between each one.  A good focus increment is 75 microns and a good number of focus steps is 7.  Then click the "Add" button.

After the exposure is done reading out, you will see an image containing lines of stars like this. 

Open a terminal on observer2 and load iraf and mscred by typing:

> cl
vocl> mscred

display the image and run the mscfocus command by typing:

mscred> cd /data_local/images/fits/2012B-9999/
(change 2012B-9999 to your proposal ID)
mscred>!ds9 &
mscred>!funpack DECam_00123456.fits.fz
mscred> mscdisp DECam_00123456.fits 1
vocl> mscfocus DECam_00123456.fits
(change DECam_00123456.fits to the focus image you just took)

You will now select stars to use to calucalate the best focus.  Place the cursor on the top star in a cleanly separated and unsaturated sequence and type the "g" key (always use the top star, regardless of whether or not there is a double step between it and its neighbor).  A window will appear displaying the FWHM as a function of focus for that star.  Type "q", place the cursor on the top star of another column, and type "g" again.  Repeat this sequence for a number of different stars.  With the cursor in the ximtool, finally type "q".  You will now see a window overlaying the focus sequences for all the stars you just measured.  If there are large outlying points, place the cursor on them and type "d", which deletes the whole star associated with that point.  Once you are satisfied, type "q", and the program calculates the best focus for you.

You can also use the command:

mscred> mscexam DECam_00123456.fits

Move the mouse over a star and type "r" and/or "e" to see the radial profile and ellipticity of the star.