[RASMB] DTT data; SEDNTERP update

[John Philo]

RASMB,
 
Thanks to Holger Strauss and his lab, we finally have density and viscosity
data for DTT, and I have now calculated the polynomial coefficients needed
to put those data into the SEDNTERP database. If you need to enter those
manually, I've put those coefficients at the end of this message, but you
shouldn't need to do that. 
 
These are the first new user-contributed data for many, many, years, and
perhaps they will inspire one of you to finally measure other things many
people want (HEPES, PIPES, trehalose, sorbitol, Tween, ...)
 
I am also now releasing version 1.09 of SEDNTERP, which will automatically
incorporate the new DTT data. I actually hadn't planned to ever release new
updates to version 1 because Tom Laue and David Hayes have been working on
version 2 for some time, but I recently found a small problem that might
lead to incorrect results (not actually a bug, but more an issue of
semantics). Let me explain:
 
When you press the 'Print Summary Report' button from the Sample Composition
form that printout has always included the "mean residue weight", along with
many other things. That value has always been literally what it says, i.e.
the molecular weight divided by the total number of amino acids. However,
within the circular dichroism community a quantity that is often called
"mean residue weight" is actually the molecular weight per peptide bond,
i.e. MW divided by (total amino acids - 1). To further add to the confusion,
some people in the CD field use the first definition, some the second. If
you are working with a protein of 100 amino acids or more the difference
between the two definitions will be 1% or less and thus less than the
experimental error, so one can easily just ignore this distinction. However
if you are working with a small peptide these two numbers will be
significantly different, and using the wrong one would affect the fraction
alpha helix etc. that one computes. Therefore version 1.09 now prints both
numbers (per residue and per peptide bond), and you can use whichever makes
sense for your purposes.
 
As many of you are aware, there has been a problem arising under Windows XP
that causes a crash after an "illegal function call" message when you try to
bring up the buffer composition dialog box. This is a Microsoft
compatibility issue that I can't directly fix---Windows XP actually runs the
code in the wrong order! However for some reason (dumb luck?) I have not yet
seen this crash with the new version. If you are still having this problem,
try using the File...New command before you do anything else, which seemed
to help for version 1.08.
 
The easiest way to update SEDNTERP, and simultaneously add the new DTT data,
is to download a self-extracting updating file sdnupdat.exe, either from
<http://www.jphilo.mailway.com/download.htm>
http://www.jphilo.mailway.com/download.htm or the RASMB archive,
<http://www.rasmb.bbri.org/rasmb/windows/sednterp-philo/>
http://www.rasmb.bbri.org/rasmb/windows/sednterp-philo/. Alternatively you
can download the full version (sdtr0601.exe) and install it into the
existing folder. The first time you run the new version it will detect the
database update, bring up a dialog box saying it is updating to revision
level 1.1, and then will add the new DTT data.
 
Best regards to all,
 
John
 
----------------------------------
Database entries for DTT density:
a = 0.9982
b = 0
c = 4.15428
d = 0
e = 0
f = 0
Cmax = 0.13
Max error = 0.5
Source = Holger Strauss
 
Database entries for DTT viscosity:
a = 1.0000
b = 0
c = 28.824
d = 0
e = 0
Cmax = 0.13
Max error = 1.5
Source = Holger Strauss
 
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