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dm version 2.0 beta release
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*** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
I've put a beta release of dm 2.0 on the ftp site here if anyone wants
to try it out. New features include:
1. The Perturbation Gamma Correction. This is an extension of the
gamma correction of Abrahams (Acta Cryst, D53, 371-376) to arbitrary
density modification methods.
The bias of the modified map with respect to the initial map is
estimated by applying a perturbation to the initial map and measuring
the corresponding perturbation in the modified map. This allows
extension of the gamma correction to methods such as histogram
matching for which theroetical estimates of gamma break down. The
perturbation can also be estimated for subclasses of reflections,
allowing for example a gamma correction which varies as a function of
resolution, which is necessary for multi-resolution modification.
The resulting phases are better than for reflection omit mode, since
it is not necessary to omit large batches of reflections. Results are
also obtained in a fraction of the time. As a result this is now the
recommended mode for all calculations, including averaging.
2. Input solvent and averaging masks can be recalculated after a
given number of cycles, allowing refinement of averaging masks and
input solvent masks.
3. The logfile is now in HTML, with log-graphs displayed inline using
a Java applet (as long as the Java classes are installed correctly).
4. It is now possible to disable or weight down phase combination,
for example where there is good NCS and initial phasing is from MR.
5. Some of the more pernicious failures have been fixed.
This is a beta release, there are probably bugs which I have not
picked up in my testing so far.
Instructions for fetching and installing the code are given below:
> ftp ftp.yorvic.york.ac.uk
ftp > cd pub/ccp4
ftp > get dm.tar.gz
ftp > quit
> gunzip dm.tar.gz
> tar xvf dm.tar
> cd dm/src