[RASMB] For SOMO users - New ASAB1 version

[Mattia Rocco]

Dear SOMO users,

we have fixed a couple of bugs to the programs ASAB1:

1 - In particular, it is NO LONGER needed to manually edit the 
SOMO-generated main file to add a value for the partial specific volume 
after ASAB1 re-check. That is, you can insert the PSV value when prompted 
by SOMO. The new ASAB1 version properly recognizes this field on re-check.

2 - We discovered a mistake in the bead assignment routine when the atom 
listing in the PDB file was not following the usual N-CA-C-O-side chain 
sequence. This has been fixed. In any case, it seems that this problem had 
practically NO EFFECT on the computed hydrodynamic values, likely because 
of internal compensation. Nevertheless, we strongly advise to substitute 
you current version of ASAB1 with the new one.

The new ASAB1 executable can be downloaded as a stand-alone module from 
Marcelo Nollmann's Berkeley SOMO webpage:

http://mcb.berkeley.edu/labs/cozzarelli/somo_new/index.html

click Installation/Downloading, then ASA under the big ASA header. 
Substitute your previous asab1 version with this file. Upon launching, 
check the header, it should say "Version 3.5, August 2006"

There is also a trial version of ASAB1 for Windows using Cygwin, but we're 
still working on it. The new ASAB1 for Linux is also included in the full 
SOMO suite.

Let us know of any problems!

Cheers,

Mattia, Marcelo, Olwyn.