A SHORT guide to MAXUS

About the program

The following is a stepwise guide to use MAXUS program. Normally you will get the final data as "import.cif" file, inside a maxus directory which is inside the directory where the data was processed. You have to be in the correct directory to start the program.

• Starting the program: (from Tungsten):
  • You have to open a window/shell.
  • Change to the appropriate directory (by the command such as "cd data/sample1/maxus").
  • Start the MAXUS program by the command "maxus".

• Starting the program: (from other Unix or Linux):
  • You have to open a window/shell.
  • xhost tungsten.chem.umass.edu
  • ssh username@tungsten.chem.umass.edu
  • Login using your password (you should have an account).
  • setenv DISPLAY yourcomputerfullname_or_IPaddress:0.0
  • Change to the appropriate directory (by the command such as "cd data/sample1/maxus").
  • Start the MAXUS program by the command "maxus".

• Importing the data:
  • Click File-->Import-->CIF

• Getting the Space Group:
  • Click Init-->Space group (and follow it till the end) -OR-
  • Click Auto-->Space group
  • Manual inspection at the suggested space group is VERY important.

• Solving the Structure:
  • Click Solve-->SIR-->Default1 (or any other) -OR-
  • Click Auto-->Solve
  • Structure Solution works very well if the Formula is close to perfect!
  • In some cases ALL the methods fail! Then get some tips from some expert.

• Viewing/Editing the Structure/Model:
  • Click Model-->Display (or Display expanded)
  • Rotate by clicking on X, Y or Z buttons
  • See the peak heights by clicking "Info"
  • Assign atoms by clicking on the element from the periodic table and then clicking on the atom you want to change.
  • Delete unwanted peaks by clicking delete button and clicking on unwanted peaks one by one.
  • When in the "Info" mode, click on any atom and type-in a number for it and <enter>.
  • To come out of the "Info" mode, click "Clear".
  • Learn about all the options available through the buttons.
  • When done, click "Save & Exit" (or "Abort", if you do not want to save).
  • If you can not Exit, then you may have two atoms with same symbol and number, which must be corrected!

• Refining the Structure:
  • Click Refine-->Lsq-->deafult.
  • Local recommendation: change the "Cut-off" to 0 (zero) and the "Min sin(th)/lam" value to 0.13 (from 0.0).
  • Click "OK" & "Exec" & "OK". ----OR----
  • Click Refine-->SHELXL-->deafult.

• checking the difference Fourier:
  • Click Fourier-->Fourier-->Give # of peaks (20); click "OK"
  • If you had used SHELXL, it has been done along with refinement
  • Then use the "Model" Routine (see above) to view/edit the new peaks.

• Applying ANISOtropic Atomic Displacement Parameters (ADP):
  • Click Model-->Display.
  • Click Properties and select Atom Type.
  • Click on any atom for each element, Select Aniso and click on Apply.
  • When all atoms showing I (isotropic ADP) are changed to A, click Return.
  • When done, click "Save & Exit".
  • Continue the refinement (as shown above).

• Adding Hydrogen atoms at calculated positions:
  • This should be done after proper labeling, because the hydrogens will be automatically assigned numbers based on the parent atom.
  • Click Model-->Display.
  • Click H-Addition.
  • Click on a atom and Select correct number of Hydrogens to be added.
  • Click on Apply. Repeat for all the atoms that need hydrogens (see warning below).
  • When all the Hydrogens are added, click Return (to come out of "H-Addition" menu).
  • When "Save & Exit" is clicked, the hydrogens also will be saved.
  • Continue the refinement (as shown above), but change the following:
  • It is recommended that during refinement, the hydrogen atoms be assigned a Thermal Parameter of "parent+0.02". To do this, select "Customize H Atoms" in the LSQ menu and in the button besides "Thermal:" select "Parent+" and "OK". (When you Exit Maxus, the customizing is forgotten and needs to be done again when/if the refinement is continued later).
  • Warning: This hydrogen fixing looks to be outdated, at least when compared to SHELXL-93 (1993 release itself!). The distances are rather poor and also the method is not that good. We know that this program fixes hydrogen for five-membered aromatic rings in a worst way. So, do not use this program if you have such a ring system and also verify if they look geometrically proper in all rings, except six-membered rings.
  • Also, hydrogens can not be fixed for: hydroxyl groups, aliphatic amino groups, disordered atoms and atoms adjacent to disordered atoms. It is rather difficult to fix hydrogens for a methyl group on a mirror symmetry. These are common problems, not specific for Maxus alone. If the data is very good, the hydrogens for OH, NH2 groups can be located from Difference Fourier (see above).

• Graphics:
  • Click Graphics-->Ortep-->view model (or view expanded) -OR-
  • Click Graphics-->any other choice-->
  • Use the menu's available to rotate, label and to change other options.
  • Once you get satisfactory orientation in ORTEP, you can move the labels.
  • Usually the labels can be moved by pressing and dragging the middle mouse button (if it works!).

• Getting the CIF file:
  • This should be done after final refinement and then running a difference Fourier (see above).
  • Click Publish-->CIF-->Create
  • Check all the choices provided in the first button and edit/delete the defaults.
  • Edit all the default values in the bottom 4 boxes.
  • Click "OK".
  • Select "No" when asked about including reflection data.
  • The CIF file will be created with the name "full.cif"
  • If SHELXL was used for refinement, the file will be created automatically and it will be called "shelxl.cif".