[3dem] Bsoft 1.5.0

[Bernard Heymann]

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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