The program can be obtained in both "build-it-yourself" (i.e. source code) and pre-built (i.e. compiled and linked) versions from the LMB web site. The only major difference between the two versions is that the pre-built versions include the Kabsch REFIX autoindexing whereas the source code does not; if you require the Kabsch indexing and you want to build the program yourself, e-mail us with your request.
N.B. The new interface iMosflm does not use the REFIX autoindexing, so it is not necessary to include it in your build.
The program is free to both academics and industry.
The current reference is;
A.G.W. Leslie and H.R. Powell (2007), Evolving Methods for Macromolecular Crystallography, 245, 41-51 ISBN 978-1-4020-6314-5
The title of the paper is
Processing Diffraction Data with MosflmIf you want to read it, here's a link to Springer's online copy (which may be downloaded as a PDF).
MOSFLM version 7.0.5 has been built and tested with CCP4 version 6.1.2. We recommend not trying to build with earlier versions.
MOSFLM v7.0.5 has been compiled and run on the following systems;
Mosflm has, in the past been built and run on the following obsolete platforms:
If you have a single image which you want to produce a JPEG file from, use the following command-line options in Mosflm (type the black bits; stuff echoed to the screen is in green;
Here's a C-shell script to create a movie (as a GIF) from 40 images - you need to have ImageMagick installed to do this.MOSFLM => image test_1_001.img MOSFLM => xgui on New gui stuff switched on MOSFLM => goloads of interesting output regarding the image...NeoCtrl =>CREATE_IMAGE BINARY TRUE FILENAME intermediate.jpgIf you want to produce mime-encoded images, just leave out the "BINARY TRUE".Either way, the command is followed by more interesting details on the JPEG, ending with:
JPEG QUALITY = 85 JPEG COMPLETE NeoCtrl =>return MOSFLM => exitYou can now use this JPEG just like any other. If you produced a MIME encoded JPEG, here's a perlscript to translate this (put it in a file called ./mimedecode.pl;#!/usr/bin/perl use MIME::Base64 qw(decode_base64); local($/) = undef; # slurp print decode_base64(<STDIN>);then make it executable and run...chmod +x mimedecode.pl ./mimedecode.pl < intermediate.hqx > image.jpg
#!/bin/csh -f
set ident = "lys_fine"
set exten = "pck"
set MOSFLM = ipmosflm
foreach I ( 01 02 03 04 05 06 07 08 09 \
10 11 12 13 14 15 16 17 18 19 \
20 21 22 23 24 25 26 27 28 29 \
30 31 32 33 34 35 36 37 38 39 40 )
echo making image no. ${I}
$MOSFLM << EOF
image ${ident}_0${I}.${exten}
DETECTOR MAR
xgui on
go
CREATE_IMAGE BINARY TRUE FILENAME intermediate.jpg
return
exit
exit
EOF
#
# and shrink it, making a new JPEG
#
convert -geometry 512x512 intermediate.jpg ${ident}_0${I}.jpg
echo finished image no. ${I}
end
#
#create the animated GIF
#
convert -delay 10 ${ident}_0*.jpg ${ident}_mov.gif
#
# tidy up the intermediate files
#
/bin/rm -f intermediate.jpg
There are many other utilities to create a movie from a series of JPEGs - my personal
favourite is Quicktime Pro, but that costs $$$.
setenv MOSFLM_VERSION_NUMBERS TRUEor for sh/ksh/bash
MOSFLM_VERSION_NUMBERS=TRUE
export MOSFLM_VERSION_NUMBERS
Releases of MOSFLM prior to version 6.00 (i.e. until sometime late in the last Century) sometimes had difficulties in autoindexing images, so it was relatively common to use Denzo for the autoindexing stage. Since v6.00, this should no longer be necessary!
There are now two solutions to the problem of getting the [A] matrix in MOSFLM form;
Disclaimer:
These pages are my personal pages. The opinions expressed here are not necessarily those of the Laboratory of Molecular Biology or the Medical Research Council.