Indexing in Crystallography: ipmosflm
The process of indexing is determining the space group from your diffraction pattern. The points of intensity that are hopefully present in your diffraction pattern, I will refer to as spots.
The following are the very basic steps needed to index your diffraction pattern. You made need more advanced commands depending on your data in which you should refer to the ipmosflm documentation.
The process of indexing with ipmosflm loosely moves from top to bottom of the gui.
Initially, you should cover the beam stop or any other shadows on your diffraction image. Use Beam / mask images, which is the bottom button of the gui.
1) Find where the spots are located
-click Read Image (can select an image), Find Spots
2) Move to another image to find spots
-click Read Image (select a different image), Find Spots
(you may get better results by selecting images located away from each other)
(if you have between 200-700 spots then proceed to the next step)
3) Select images to index
-click Select images and select the images from the corresponding number listed
(the program usually detects which images it should use, but best to make sure)
4) Autoindex
-select the best solution, lets start with the default
(you need to type both the solution number and then enter the space group)
(I have found it best to select lower symmetry since it can be increased later)
5) Predict the location of where the spots should be located based on your autoindexing
-click Predict
(if they do not match then you could have a number of issues: 1) wrong space group 2) cracked crystal 3) wrong beam center 4) wrong rotational parameters)
-click Clear prediction (remove the spots that you just predicted)
6) Estimate mosiacity
-the lower this number the better (looking for number around .4-1.2)
7) Refine Cell
Integration
(keep an eye on the integration despite it maybe boring sometimes the crystal may drift during collection or some other issue)
Rarely will you ever have to significantly vary from the default inputs. If you are new to using ipmosflm, I would recommend simply working with the default options to gain a sense of how the program functions. Followed by examining what each option means – ie. don’t become intimidated by all the options to the point of not giving it a try (as long as you have images you can always start over).
