An Introduction to Mosflm (1) what Mosflm does (2) where it fits in the crystallography process (3) run through a typical job (4) introduction to the CCP4.

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Presentation transcript:

An Introduction to Mosflm (1) what Mosflm does (2) where it fits in the crystallography process (3) run through a typical job (4) introduction to the CCP4 Mosflm tutorial

What Mosflm does indexes images (singly or together) estimates the mosaic spread refines crystal parameters accurately calculates data collection strategy integrate a series of images provides statistics on the processing

estimate mosaic spread strategy refine cell integrate integrate single imageindex The X-ray Experiment (1) SCALA crystalcollect initial image(s)X-rayscollect rest of dataset scale phase

estimate mosaic spread refine cell integrate integrate single imageindex The X-ray Experiment (2) SCALA crystalcollect image(s)X-rays scale phase

A brief aside: Optimization of Data Collection Pre-process at least one image (preferably two at 90º to each other) to obtain: Cell parameters, crystal orientation and putative Laue group Estimate of mosaicity Effective resolution limit Crystal to detector distance Exposure time Strategy for data collection Remember! This is the last experimental stage - if you collect bad data now you are stuck with it. No data processing program can rescue the irredeemable!

What is needed prior to running Mosflm ? X-ray images Experimental details (e.g. detector type, direct beam position, wavelength, etc) The program itself and a computer to run it on!

[localhost:~/test/muldlx1] harry% mosflm ************ Version for Image plate and CCD data 11th March 2005 *********** A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann (1998) J. Appl. Cryst. 30, Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993), J.Appl.Cryst. 24, ) X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.) (Campbell,J.W. (1995) J. Appl. Cryst. 28, MOSFLM => image muldlx1_301.mar2000 MOSFLM => go From information in the image file, the detector has been recognized as: Mar Image Plate If this is incorrect you must supply a DETECTOR keyword Crystal to detector distance of mm taken from image header Wavelength of A taken from image header Pixel size of mm taken from image header. Start and end phi values for image 1 from image header are and degrees. image FILENAME: muldlx1_301.mar2000 The red circle denotes the region behind the backstop shadow (Use BACKSTOP keyword to set this.)

live demo here

Checking the output There are two useful log files; SUMMARY ; this is of most use when viewed with the CCP4 graph viewer LOGGRAPH, as it contains graphs of parameters which have varied through the data processing. mosflm.lp ; this can be very large, and contains a complete record of the experiment.

introduce tutorial here