Recent improvements to Mosflm - version 6.11
Harry Powell, MRC-LMB, Hills Road, Cambridge, CB2 2QH
Mosflm version 6.11 was released recently. It includes many small bug
fixes and improvements over previous releases. This article describes
the improvements introduced since the release of version 6.01 in July
1999 (see CCP4 Newsletter 37, October 1999).
Further information about the program can be found at
including an on-line keyword search and brief command synopsis
to complement the help document and user guide.
New and improved features
The spot-finding routines have been improved and the DPS autoindexing
code has been modified to search for more likely combinations of basis
vectors. This results in more robust autoindexing and allows more
rapid generation of the set of reciprocal lattice projections. In
addition, the DPS autoindexing estimates the longest
cell edge likely by analysing the spot separation
and the detector parameters rather than assuming a
In order to aid discrimination of correct solutions, the user can now
choose to pre-refine the autoindexing solutions before making a
Autoindexing using the DPS code can now be performed without the
GUI running, using the AUTOINDEX DPS keyword pair. A
number of options are available to the user and described
in the user guide, viz:
unknown cell - default mode, no extra keywords required
known space group, unknown cell - needs SYMM keyword
known space group and cell - needs SYMM and CELL keywords
prerefine solutions to aid discrimination - needs REFINE subkeyword on
the AUTOINDEX DPS line
choosing a particular solution from the list - needs SOLUTION subkeyword on
the AUTOINDEX DPS line
In releases of Mosflm prior to version 6.10, post-refinement of cell
and detector parameters could only be performed when a reasonable
number of reflections were partial over only two adjacent images; this
limitation has now been removed so that reflections spread over many
images can now be used. This allows correct processing of fine-phi
sliced data or images with high mosaicity.
Estimation of mosaicity routine included. Once an image has been
indexed, it is now possible for the program to calculate an initial
estimate of the mosaicity of that image.
The main log file produced by the program can now be written with a
version number from 1 - 99 by setting the environment variable
be TRUE. This can avoid the sometimes annoying problem
caused when the log file is overwritten when the program is run.
Several new image formats have been introduced from version 6.10; the
most important is the CBF file. This is a binary representation of an
IUCr agreed standard, the imgCIF. The principle advantages of this
over other images are that it is portable between detxector types and
comprehensive experimental information is included in the image file
in a uniform way. This is good news for users for two principle
The following specific image types can now be processed; DIP 2040, R-Axis V,
Oxford PX210 CCD and Brandeis 2x2 CCD.
written as CBFs are processable by a single version of any program
which supports the format;
CBF files produced by a novel detector can be processed by any CBF
compatible program and neither the program nor file should need
CBF files contain all information relevant to an experiment,
e.g. wavelength of radiation, polarization, beam centre, oscillation
angle etc., so users are no longer dependent on their notebooks for
Programmers working for the CCP4 in Daresbury have identified and
corrected several long-standing errors in the XDL_VIEW code which have
caused a variety of problems in porting Mosflm to new platforms. These robust
bug fixes mean that Mosflm can now run on Linux PCs using 24- and 32-bpp colour
and separate XDL_VIEW code is no longer needed for Compaq Alpha
workstations with the 4D60T (and similar) graphics
Data harvesting code (written by Kim Henrick, EBI) has been included
to help with tracking of experimental method and results.
The building and installation of Mosflm has been rationalized. A
build shell command file sources
to set compilation and linking flags for different platforms. These
files can be modified easily with a text editor for new platforms.
Since CCP4 version 4.1, Mosflm has been distributed with the CCP4
suite and is
ftp://ccp4a.dl.ac.uk/pub/ccp4 as well as via the MRC-LMB website.