Download Bsoft

Version 1.5.4

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  • PFT2/EM3DR2
    
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• Bshow
  • Main window
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  • Fitting the CTF
  • Picking particles
  • Picking filaments
  • Tomography
  • Crystallography
  • Helical processing
  • Model
    
• How to
  
  • Unix command line
    
  • VMS command line
    
  • Simple image manipulations
  • Map synthesis
    
  • CTF fitting
  • Micrograph pair alignment
  • Resolution estimation
  • Handedness determination
  • 3D particle picking
  • Sequence analysis
    
• Workflows
  
  • Single particle analysis
    
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• Distributed processing
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Source code

The gzipped tar archive version 1.5.4 (~6 Mb):

bsoft1_5_4 .tgz

The tar archive version 1.5.4 (~20 Mb):

bsoft1_5_4 .tar

Apart from the major releases, there are development snapshots available. These archives are not necessarily complete and need to be unpacked within an existing bsoft directory.

Platforms supported

• Linux (i386/i686, x86_64, PowerPC, Alpha, Itanium)
  
• Darwin or MacOSX (PowerPC, Intel)
  
• IRIX64 (SGI)
  
• Solaris (Sun)
  
• AIX (IBM)
  
• OSF1 or Tru64 (Alpha)
  
• VMS (Alpha)
  
• Cygwin_NT (Windows NT)

In principle the package could be compiled on any Unix-based operating system.

 

Requirements

The Z library:

The inclusion of the PNG format in Bsoft requires libz for compression. The required files are:

• /usr/include/zlib.h or /usr/local/include/zlib.h
  
• /usr/lib/libz.* (such as libz.a or libz.so)
  

On some versions of Unix and VMS, libz may not be available, therefore it is included in the distribution and will be compiled.

Tcl/Tk:

Bsoft is primarily a command-line package, with all the necessary code included in the package. However, from version 0.9, it includes a Tcl/Tk interface and a Tcl/Tk script, bshow, useful for the display of images and a few interactive manipulations (not available for VMS). The Tcl/Tk version must be 8.3 or higher. Bsoft can be compiled without Tcl/Tk (see below for details).
On most Unix boxes, the Tcl/Tk headers and libraries are installed in either /usr or /usr/local (look for /usr/include/tk.h or /usr/local/include/tk.h). The Bsoft compiler script, bmake, tries to find the Tcl/Tk headers automatically. Make sure the Tcl/Tk version is 8.3 or higher. There may be a version suitable for installation under VMS, but try at your own risk. Make sure the commands "tcl" and "wish" are in your executable path.

Tcl/Tk is part of the system for Mac OSX 10.4 and later. For earlier versions of Mac OSX, a suitable Tcl/Tk distribution can be obtained from:

http://sourceforge.net/projects/tcl/

Under "Latest File Releases" click on the "download" link for Tcl and download the disk image (or a similar, newer distribution):

TclTkAqua-8.4.6.dmg

Mount the disk image, click on the "TclTkAqua.mpkg" icon and follow the instructions. The following will be installed:

/Applications/Wish Shell
/Library/Frameworks/tcl.framework
/Library/Frameworks/tk.framework

Bernard Heymann 20080306