From: John Philo <jphilo@mailway.com>
  To  : rasmb@alpha.bbri.org
  Date: Mon, 20 Mar 2000 21:33:51 -0800

RE: SEDNTERP update

As a follow-up to Tom's message, there is one other bug fix in the new
version that he didn't mention.

In prior versions there was sometimes a problem in the graphs of ellipsoid
axial ratios versus hydration. The graphs for prolate ellipsoids using the
Teller method or oblate ellipsoids using the vbar method were okay. However
for the prolate/vbar or oblate/Teller combinations I messed up the logic,
and hence the data displayed on the graph was actually for the other of
those two combinations. This is now fixed too. The data shown on the Results
page were okay.

Lastly, I wanted to remind SEDNTERP users that if you publish or export the
graphs showing the shape of ellipsoids (or cylinders) you must be careful
not to distort the proportion of the X and Y axes. Despite the warning
messages that are issued about this, figures have appeared in print where
the X and Y axes are not the same physical length and hence the shape has
been distorted.

If you change the X/Y axis length ratio so the graph is no longer square,
your molecule will appear ellipsoidal even if the actual axial ratio is 1!
Please be careful when printing those graphs or pasting them into another
program, following the program guidance in order to preserve the aspect
ratio.

John

-----Original Message-----
From: Tom Laue [Tom.Laue@unh.edu]">mailto:Tom.Laue@unh.edu]
Sent: Monday, March 20, 2000 1:21 PM
To: rasmb@alpha.bbri.org
Subject: Sednterp update


Dear RASMBers,
  While working on the update to Sednterp, John Philo found an error in the
original code from my lab. In particular, the temperature correction of the
density for heavy isotopes was wrong: the melting point of the isotope was
used instead of the temperature of maximum density in the calculations.
  Some quick testing by John indicates that the miscalculation for pure D2O
would produce errors of ~.003 in rho. This error, in turn, propogates to a
~1.1% error in the mass estimate for a protein with a vbar = 0.73 ml/g.
  To give you a better idea of the level of imprecision, here are values
John calculated for pure D20 at different temperatures:

T	old code	new code	CRC(Kell data, not formula)
5	1.10601	1.10564	1.10562
10	1.10569	1.10601	1.10599
20	1.10392	1.10537	1.10534
30	1.10091	1.10325	1.10323
40	1.09689	1.09997	1.09996

  There are two ways to update Sednterp with this problem patched. The new
full install is the file sdtr0002.exe (1.8 MB). Since only the program
executable is changed, there is also a file sdnupdat.exe (220 KB) which
updates versions 1.01-1.04 to 1.05. The update-only file does not have a
true installation utility; when the self-extracting archive is run you must
supply the correct folder location for the previous SEDNTERP installation
(usually c:\sednterp) and the archive will overwrite the older program file.
  Both the full update and the patches are available from either John
Philo's site or the RASMB ftp site:
http://www.jphilo.mailway.com/download.htm
ftp://alpha.bbri.org/rasmb/spin/ms_dos/sednterp-philo/
  If you do a full re-install, you must be careful not to overwrite your own
databases (make a backup of SEDNTERP.MDB and PHYCONST.MDB just in case, and
answer YES that you want to preserve your existing databases when you get
the prompts).
  My apologies to everyone for allowing this error, and my thanks to John
Philo for finding and fixing it.
Tom
--------------------------------------------
Tom Laue
Professor and Director of the Center to Advance Molecular Interaction
Science
University of New Hampshire
Biochemistry and Molecular Biology
Rudman-379
46 College Rd.
Durham, NH 03824-3544

Phone: 603-862-2459
FAX:   603-862-4013
---------------------------------------------