Getting started with Mosflm

• version 6.2.2, installed independently of CCP4 is considered to be the most stable version
• version 6.10 is now included in CCP4 version 4.1.1
• Do source /prog/setup mosflm (equivalent to mosflm_6.2.2) or
  or source /prog/setup mosflm_6.11 or
  or source /prog/setup mosflm_6.01 to set up the environment.
• MOSFLM web site
• MOSFLM web site copy of manual
• Local copy of mosflm manual (HTML)
• mosflm's help command (HTML)

First of all as usual, be sure to do source /prog/setup mosflm to set up the environment, which will also make sure that CCP4 is set up.

Mosflm has a graphical user interface showing the image as well as some parameters and a menu of commands. Before this appears, though, you need to specify at least the detector type and image file name on the command line in order to start the display.

In order to do the autoindexing mosflm will also need to know the direct beam position, the oscillation angle and the crystal to detector distance. The latter two are not read from the R-Axis IIc files so those must be entered on the command line or on the parameter menu. (see below for an example). Mosflm assumes a wavelength of 1.5418Å (Copper Kalpha) unless told otherwise. While it may be able to read some of this information from the image file, you should be sure it was correctly entered in the R-Axis data collection form.

By default, mosflm expects an image filename composed of some sort of core followed by a hypen (-) or underscore (_), which in turn is followed by an image number and file type (e.g. file_001.osc). If you did not use this format, then you can specify the format of the image file name using the template command.

Type mosflm to start the program and then enter the following commands and their parameters:

• detector raxis <or raxis4>
• distance distance
• image filename

  or, because mosflm expects a hypen (-) or underscore (_) separating the file name from the image number and you might not have done that:

  • template filename###.osc
  • image 1 <or whatever number should be in place of the above ###'s>

  If the R-Axis IIc was used, then you will need to specify the phi angle and range with the image command line. For example:

  • image 1 phi 0.0 to 1.5