P212121

Mosflm was originally developed by Andrew G.W. Leslie and is now being updated by Harry Powell at MRC Laboratory of Molecular Biology.

Mosflm can process diffraction images from a wide range of detectors and produces, as output, an MTZ file of reflection indices with their intensities and standard deviations (and other parameters). This MTZ file is passed onto other programs of the CCP4 program suite (SORTMTZ, SCALA, TRUNCATE) for further data reduction (reference).

In addition, Harry has a page dedicated toward help and guidance using mosflm which can be found here.

To get started using mosflm (assuming mosflm has already been installed) you have to open a terminal then type ‘ipmosflm’ or ‘imosflm’ (you don’t need a comm file if you are using iMosflm) depending on which version you would like to use. Here is a list of the basic linux commands that you will need to use the program.

This information is also available in the MOSFLM 7.0.4 User Guide. My goal here is to have a comm file that you can simply copy/paste/edit. A “comm file” is a file that allows mosflm to understand inputs specific to your experiment that may vary between users (such as what you named your files or where they are located).

A comm file is simply a text file, which can be generated by typing ‘edit’ into your terminal. Once completed save this file in the directory in which you plan to run mosflm. Save the file with the name ‘comm’ so it is easy to remember when you need to refer to the document using mosflm.

If you would like more information about creating a comm file, you may find this link help.

Below is a hypothical example of what your comm file should contain:
detector marccd (type of dectector used during collection)
findspots threshold 15 (threshold to search for spots this is a good default, but can adjust later)
synchrotron polarisation 1.00 (wavelength used during collection)
directory /home/data/lyso (location of the data)
template lyso_### (what the data files are named)
image 1 phi 0 0.3 (the number of the 1st image, usually 1 and the step size along phi in this case)

The # symbols stand for any number which allows all your images to be read into mosflm.

This is a blank comm file that you will need to fill with your experimental data:
detector
findspots threshold
synchrotron polarisation
directory
template
image 1 phi

You may also need other inputs depending on if your image header was correctly formatted which would include:
distance 120.00
beam 84.444 84.824
pixel 0.0792