New density modification program

Dave Love at
Thu Jul 28 04:46:18 EST 1994

Since there are periodic enquiries about `squash' here, I'm re-posting
this announcement of an alternative program from the CCP4 mailing list
in the hope it will be useful and generate helpful feedback.  In case
you don't already have the CCP4 suite, note that dm needs linking with
the CCP4 library (from the same source) and uses CCP4-format files, so
probably makes most sense in conjunction with the other CCP4 programs
(plug, plug).

[Send dm-specific mail to Kevin Cowtan (address below) and more
general enquiries to the ccp4 address.]



'dm' is a density modification program written as a part of the CCP4 library
and distributed under the CCP4 license. It will be included in the next
release of CCP4, and is available now in beta release by anonymous ftp

'dm' is a single program which will take an input .mtz file, perform a
variety of density modification techniques, phase recombination, and
recycling, and output improved phases to a new .mtz file.

Current facilities include:
 -  Solvent flattening ('Wang-ing'), including:
      Automatic mask calculation or user mask input.
      Output of final mask.
 -  Histogram mapping.
 -  NCS averaging, including:
      Multi-domain averaging.
      Improper symmetries.
      Refinement of ncs matrices.
      User input masks.
 -  Fragment recycling and partial structures.
 -  Sayre's equation.

The program is controlled through standard CCP4 card input files, with
many parameters set automatically or taking sensible defaults, so that
a typical script will have less than 10 lines (excluding averaging

'dm' has also been designed as a testbed for new density modification
ideas: Currently under investigation is the indentification of the
critical points in the density map as a new means of skeletonisation.
It is hoped that this will lead to a density modification technique
like that successfully employed in PRISM. A new technique involving
a two-dimensional histogram is also under development to replace the
existing histogram mapping method.

This package has been produced by Kevin Cowtan, in collaboration with
Peter Main, Richard Leggott, David Shuller, David Love, Eleanor Dodson,
Erid Grosse, and with help from Pete Dunten, and Phil Evans. The project
has been supported by CCP4 and by the University of York, England.

To pick up the package, anonymous ftp to as follows:
> ftp
Name(..):  anonymous
password:  (your email address)
ftp> cd pub/ccp4
ftp> get dm.tar.Z
ftp> quit
> uncompress dm.tar.Z
> tar xvf dm.tar
and read the file dm/READ.ME. If you have any problems, please email me at
cowtan at                                      KEVIN COWTAN



--Dave (not the secretary)

Thank you for your interest in the CCP4 protein crystallography programs.

 Secretary to CCP4      | Telephone: (+44) 925 603530  (direct line) 
 Daresbury Laboratory   |            (+44) 925 603000  (switchboard)
 Warrington WA4 4AD     | Facsimile: (+44) 925 603124
 UK                     | e-mail:    ccp4 at

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