[RASMB] RE: DC/Dt vs. sedfit

[John Philo]

RASMB,

I certainly agree with Chris Chin and Patrick Brown that proper selection of
the data to be analyzed (which scans, which regions of the cell, etc.) in
sedimentation velocity experiments is something people can struggle with. I
see this often, both when I help with the new user training at Beckman, and
when I've taught SEDFIT and other packages at workshops in Connecticut and
New Hampshire. 

We've heard a lot of divergent opinions about software recently, but one
thing I think all the software developers can agree on is that all methods
will be compromised if you feed them the wrong data.

With respect to the study and data files Chris Chin shared with us, his
choice of scans to analyze using DCDT+ unfortunately led him to wrong
conclusions. As a software developer that represents a problem that must be
solved, and I believe it has been. By coincidence this whole discussion
arose just as I was reaching completion on a project to address exactly
these issues, one that I have been working on intermittently for over 5
years.

I have just released version 2 of DCDT+, which addresses these issues on
five different fronts:

1) A new algorithm for generating the theoretical fitting function
completely removes the systematic errors that formerly arose if you chose
too broad a time span of data. This allows you to use a greater number of
scans to improve the signal/noise ratio when needed.

2) The program can now AUTOMATICALLY select an appropriate group of scans
for analysis. That selection may not be perfectly optimum for your
particular sample, but it will immediately put you into the right ballpark
for obtaining the properties of the major component(s).

3) In this version you can simply load the entire run in one operation and
then use slider controls to select the scans you wish to analyze, with an
immediate display of the resulting dc/dt curves as you 'tune' through the
run.

4) The entirely new user interface allows multiple analysis documents to be
open at one time. If you want to try analyzing different scans from the same
run, simply push the 'clone' button on the toolbar to make a copy of your
existing analysis, re-adjust the sliders in that window to select scans as
desired, and you can then compare the results while having both analyses
open simultaneously.

5) The Help file has been re-written with more extensive tutorials and
screen shots, and reformatted to make it more user-friendly and easier to
read. A version formatted for printing a user manual is also now available
to registered users. (Getting users to actually read documentation is
however a problem no software developer has yet solved!)

The enclosed study/tutorial re-analyzes Chris Chin's data using this new
version of DCDT+, as well as using SEDFIT. This document demonstrates that
DCDT+ does indeed give the correct answers even if you choose to analyze the
entire run, as Chris had done, rather than a 'snapshot' cluster of scans
that is typically used for this method. My re-analysis also shows that the
c(s) analysis conclusions are sensitive to exactly how the data is fitted
(even when using the same scans); my analysis implies a minor second species
is present.

I will follow this shortly with a second e-mail regarding the update to
DCDT+ and how to download a trial copy (the 60-day trial on this version is
independent of any earlier trials for versions 1.xx).

John



-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of Chin, Christopher
Sent: Thursday, February 16, 2006 8:27 AM
To: Patrick
Cc: rasmb at server1.bbri.org
Subject: [RASMB] RE: DC/Dt vs. sedfit


Dear Patrick,

Thank you for asking. I have the same feeling as you do and that is
motivation for me to undertake and initial this project on my spare time.

All the best,

Chris

 

 

 

 

------------------------------------------------------------

Christopher Chin

Manager, Macromolecular Assembly Core

Sealy Center for Structural Biology and 
Molecular Biophysics 

Department of Biochemistry & Molecular Biology

5134 MRB. rt1055

UTMB, Galveston, TX  cchin at utmb.edu, 

409-772-1693, efax 630-604-3416

-------------------------------------------------------------



-----Original Message-----
From: Patrick [mailto:patrickhbrown at gmail.com] 
Sent: Thursday, February 16, 2006 8:47 AM
To: Chin, Christopher
Subject: DC/Dt vs. sedfit


Chris:
I would be interested in seeing your comparison between DC/Dt and Sedfit.
What is your feelings on the two software packages? I used DC/Dt while in
graduate school, but got frustrated because although it was very easy to
use, it seemed that the answer that I got depended on whether I took early,
late, or middle scans.  I liked sedfit because I could use all of my scans
and not just a couple of them.  I didn't like that I had to keep changing
which files I loaded into DCDt to try to get the correct mass range for
fitting.

Thanks,
Patrick--
Patrick H. Brown, Ph.D.
Protein Biophysics Resource
Division of Bioengineering & Physical Science, ORS National Institutes of
Health Bldg. 13, Rm. 3N17 13 South Drive Bethesda, MD 20892 - 5766
Tel: (301) 435-9371
Fax: (301) 480-1242
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