[3dem] Bsoft 1.5.0
Bernard Heymann
bernard_heymann at nih.gov
Thu Oct 25 09:28:08 PDT 2007
Bsoft 1.5.0 released
---------------------------
I am pleased to announce the availability of the next version of
Bsoft with many enhancements and fixes, including better support for
tomography and interpretation of tomograms through modeling.
Bsoft can be obtained from http://bsoft.ws
Here are a few important changes:
MRC format change:
-----------------
The byte format of the MRC specification has changed from unsigned to
signed. There is no way to detect whether an image file has the
unsigned or signed form. In Bsoft, there are two ways to switch
between signed and unsigned integer data types:
bhead -v 7 -fixtype input.mrc output.mrc
or in bshow, using the "Image/Fix type sign" menu item.
The new MRC format also includes new origin specifications. In
previous versions of Bsoft, this origin was inconsistent with the
interpretation in Chimera. This has now been fixed so that MRC and
CCP4 versions of the same map now superimpose when read into Chimera.
breconstruct:
------------
The interpretation of the magnification of single particles have been
fixed. Particles with individual magnifications are now correctly
scaled for reconstruction.
Models:
------
Previous versions of Bsoft have rudimentary treatment of models. In
this version, models have been redefined as sets of components and
links, where a component may refer to a molecular structure, or a
density map. The models themselves may be treated as pseudo-atomic
structures to allow the application of molecular modeling. Thus the
formats supported for models in Bsoft include all the molecular
formats. In addition, the Chimera marker model (cmm) format is also
supported to allow such models to be displayed in Chimera.
However, the requirements for such models go beyond the limits of
molecular formats. A STAR format specification is also available,
allowing the user to specify component orientations and selections.
This is useful in the case of locating and orienting densities such
as the ribosome in large tomograms, and assigning to each placement a
figure-of-merit.
Bernard Heymann, Research Fellow
Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH
Bethesda MD 20892-8025
Tel. 301-451-8241, Fax. 301-480-7629
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