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Recent improvements to Mosflm - version 6.11

Harry Powell, MRC-LMB, Hills Road, Cambridge, CB2 2QH
harry@mrc-lmb.cam.ac.uk

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 http://www.mrc-lmb.cam.ac.uk/harry/mosflm, including an on-line keyword search and brief command synopsis to complement the help document and user guide.

New and improved features

1. 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 default value.

   In order to aid discrimination of correct solutions, the user can now choose to pre-refine the autoindexing solutions before making a choice.

   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

2. 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.

3. 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.

4. The main log file produced by the program can now be written with a version number from 1 - 99 by setting the environment variable MOSFLM_VERSION_NUMBERS to be TRUE. This can avoid the sometimes annoying problem caused when the log file is overwritten when the program is run.

5. 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 reasons;

   • image files 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 modification.
   • 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 this information.

   The following specific image types can now be processed; DIP 2040, R-Axis V, Oxford PX210 CCD and Brandeis 2x2 CCD.

6. 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 graphics, and separate XDL_VIEW code is no longer needed for Compaq Alpha workstations with the 4D60T (and similar) graphics processors.

7. 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 include.$HOSTTYPE files 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 available from ftp://ccp4a.dl.ac.uk/pub/ccp4 as well as via the MRC-LMB website.

March 2001

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