[RASMB] DCDT+ reports
John Philo
jphilo at mailway.com
Thu Sep 12 18:57:00 PDT 2002
I'm not sure Chris's question is of general interest but since he posted it
to all I will reply to all.
The short answer is that some of that information is actually already in the
report, and the other was deliberately not there, but yes I will make the
requested changes in the next version.
The long answer:
First, it is true that the report doesn't explicitly state the rotor speed.
The intent of the report is to completely document the user inputs and
choices which directly affect the results that are being reported (which
data files were chosen, what meniscus value, density, vbar, etc.). The
intent is not necessarily to report other things that are implicitly
determined by the scan files that are being analyzed, such as rotor speed,
the elapsed time and omega-squared-t values for each scan, wavelength, etc.
That is, the intent is to make a report that documents the data analysis,
but not necessarily one that documents the experiment itself (as presumably
your lab notebook already does). Indeed, other users have said they think
the reports already contain too much information!
Remember too that all this or any other program can possibly know about your
experiment is what is in the stored data files, and the truth is they don't
necessarily contain everything that is relevant. Two examples: (1) for
absorbance data neither the scan nor log files say whether the data was
collected in step or continuous mode (if you don't have that in your
notebook, you'll never know); (2) some labs have more than one instrument,
so which one did the data come from? (hopefully that won't matter, but...)
Second, in most cases it is not true that the report does not state the
experimental temperature. That value is printed within a statement starting
"Molecular masses are based on a sample temperature of..." that appears in
different places depending on some of the fitting choices. That temperature
value is by default the temperature recorded for the last scan used in the
analysis, but since this default value can be altered by the user that value
is included in the report.
It is true that when you have chosen to convert results to s(20,w) and
D(20,w) values, the temperature listed in the report is 20 degrees rather
than the experimental temperature, because the experimental temperature no
longer directly affects the results.
I should perhaps also point out that what really documents an analysis is
using the 'Save Results to Disk' command to create a .fit file. That file
contains all of the raw scan files, header information, etc. in addition to
all the parameters and settings. It is truly 'stand alone' and will even
preserve your analysis if/when the scan files are lost are modified.
John Philo
-----Original Message-----
From: Chin, Christopher [mailto:cchin at utmb.edu]
Sent: Thursday, September 12, 2002 12:20 PM
To: 'jphilo at mailway.com'
Cc: 'rasmb at rasmb-email.bbri.org'
Subject: RE: [RASMB] Beckman data acquisition software (4.5) and Windows
9 8
John,
In a complete unrelated subject. I use your DCDT+ to do a lot of my SV data
analysis. Sometime I want to repeat the experiment that I have done a while
back. However when I pull out the old print out report, no where in the
report can I find the experimental condition that was used at the time, e.g.
rotor speed, temperature. I have to go back to look for these experimental
condition in my raw data files. It is rather inconvenient. I am wondering
can you insert these useful information into your future update of DCDT+ so
it will show up on the DCDT+ print out.
Thank you.
Chris
--------------------------------------------------------------------------
Christopher Chin
Manager, XLA-Analytical Ultracentrifugation facility
Sealy Center for Structural Biology
HBC&G, 5.134 MRB.UTMB, Galveston,Tx 77555-1055
cchin at utmb.edu, 409-772-1693, efax 708-585-1920
---------------------------------------------------------------------------
-----Original Message-----
From: John Philo [mailto:jphilo at mailway.com]
Sent: Wednesday, September 11, 2002 12:10 PM
To: Andrew Leech; rasmb at rasmb-email.bbri.org
Subject: RE: [RASMB] Beckman data acquisition software (4.5) and Windows
98
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Andrew and all,
I have been running my XL-A from Windows 98 with no problems using version
3.01h of the Beckman GUI (I doubt the version matters, but I can't swear to
that).
Rumor has it that the XL-I will run under Windows 98 too, but I would never
recommend trying to run an XL-I from anything other than a Beckman-supplied
computer because the interference camera software is very fussy.
However, I really question the argument that your computer needs upgrading.
In my opinion, the instrument controller should be just and only that, NOT a
data analysis or general purpose computer. A 120 MHz Pentium is more than
adequate to run an XL-A (mine runs on a 100 MHz). Buy yourself a new
computer for data analysis, sure, but leave the old one running the
instrument. You really don't want to do the analysis on your instrument
computer because the analysis may crash the computer and cause loss of
experimental data.
What I do is simply leave the data files on the hard drive of the instrument
computer and access them via networking (I also back up the data via the
network). If you need more data storage on your old P120 you could add
another hard drive (and upgrading its operating system to Win98 will help
there since Win95 can't deal with today's large drives).
Lastly, if you are really going to change computers you might want to wait
until Beckman releases the new 32-bit GUI that runs under Windows 2000
(although the principal advantage there is simply the better operating
system and computer, not any significant functional change in the GUI as far
as I have seen). As I understand it the release on that could be 6 months or
so, depending on when Beckman runs out of the current interference cameras,
since the new cameras won't run with the current GUI.
John Philo
-----Original Message-----
From: rasmb-admin at rasmb-email.bbri.org
[mailto:rasmb-admin at rasmb-email.bbri.org]On Behalf Of Andrew Leech
Sent: Wednesday, September 11, 2002 8:59 AM
To: rasmb at rasmb-email.bbri.org
Subject: [RASMB] Beckman data acquisition software (4.5) and Windows 98
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Hello all,
I'm planning on replacing the computer attached to our XL/A, because
it is getting slow and temperamental (it is an ageing non-Beckman P120).
I have asked the local IT staff about sorting out a Windows 95 machine,
but they tell me they would be a lot happier with Windows 98 if at all
possible. Since the software operates over a serial link, and W98 is
rather similar to W95, I wondered if anybody had tried using the Beckman
GUI (version 4.5) under W98, and with what success, or lack thereof?
Andrew
--
Dr Andrew Leech * Laboratory Manager
Technology Facility * Molecular Interactions Laboratory
Department of Biology (Area 15) * Tel : +44 (0)1904 328723
University of York * Fax : +44 (0)1904 328804
PO Box 373, York YO10 5YW * Email : apl3 at york.ac.uk
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