June 14, 2000
To: Faculty, Post-Docs, Graduate Students and Undergraduate Researchers
From: Dr. Dan McElheny, Director, NMR Facilities
Re: Online Reservation of NMR Time - Commences July 02, 2001
The purpose of this memo is to inform everyone with a possible interest
in the operation of our NMR Facilities that we will be changing from
a paper-based instrument-time reservation system to a new web-based
reservation system. This change will become effective on Monday, July
2nd. There are many issues that need to be addressed regarding this
change, and I will attempt to cover them here.
How do I access the reservation web pages? Go to the NMR Facility
website (http://www.chem.uic.edu/nmr) and click the "online-reservation"
link (this link will be activated during late June). This will open
up a new browser window with the main starting page of the reservation
system. Making reservations and viewing instrument schedules takes
place on pages accessed from the links on this starting page. Anyone
wishing to reserve instrument time will need to obtain a login ID
and password for the reservation system.
OK, so how do I get a login ID and password for the reservation
system? Dan McElheny will
make up login ID's and passwords for all the users currently checked
out on our Bruker Avance and/or Varian Mercury systems. He will email
you this information towards the end of this month. Note that this
ID and password are not (necessarily) the same as your instrument
logins. Other users will need to contact Dan to obtain an ID and
password.
What about the sign-up rules? I will be honest with everyone
and state up front that the reservation system does not check the
"legality" of an NMR time reservation. We will still be following
the same reservation guidelines, and all reservations are subject
to checking and possible deletion by NMR Facility staff. If you need
a reservation that falls outside of the NMR Facility guidelines (e.g.,
a whole day or weekend), please check with Dr. McElheny and (usually)
he will make it for you, in a fashion which gives other users adequate
notice. In addition, reservations made more than ten days ahead of
time will be deleted (unless special prior arrangements are made).
If "illegal" reservations become a big problem then we will develop
a checking system. One other item to consider is the use of "open
time." If a spectrometer is unreserved the instrument can be used
by any user. However, I strongly recommend that you always check online
prior to using an instrument, and if it's open, reserve the time you
want, even if it is only 10 - 20 minutes. This will help prevent the
possibility of someone else reserving the instrument online and then
walking to the instrument to find you already using it. In a case
such as this the person who had reserved the time will be given the
higher priority for use of the instrument. Thus, I recommend we keep
in mind a catchy new mantra: "Reserve online before using time."
Does this mean I don't have to sign a logbook anymore when I use
a spectrometer? NO!! The logbooks are still going to be used and
every user must document their actual spectrometer usage.
Rats! Well, can I at least reserve NMR time, or check the reservation
pages, from home? No, sorry, the reservation pages can only be
accessed from computers in the ".chem.uic.edu" domain. This is a security
issue. If there is a big demand for outside access we can revisit
the issue at a later date.
Everything is going to work perfectly from the start, right?
We have done a fair amount of checking and testing on the system already,
but of course it is possible that something was missed, or that something
that seems obvious to those of us working on the system turns out
to be non-obvious to the casual user. We encourage everyone to send
us your comments on the system, especially any problems you encounter.
Also, we ask that everyone keep in mind that whenever a big change
like this occurs, complications and misunderstandings might happen.
Please be patient and understanding while we all adapt to the new
system.
Who
should I thank for this great new development? All the credit
goes to Devin Sears, who worked
very hard on adapting code he obtained from Indiana University. Send
your kudos to him!
Any questions or comments please contact me.
October 12th,
2000
To: Avance Users
From: Dr. Dan
McElheny, Director, NMR Facilities
Dear Avance
Users,
The purpose
of this email is to address a couple of issues that have arisen recently,
and also to brief everyone on a couple of new developments in our
NMR Facilities.
1. Powering
down or otherwise rebooting the SGI computers.
There have been
a couple of instances lately where an NMR user has taken it upon themselves
to force the NMR's host computer to reboot by turning off its power.
Therefore, I am forced to articulate the following policy:
It is absolutely
unacceptable for NMR users to forcibly reboot the Avance system host
computers by powering them down or by otherwise resetting them.
Under no
circumstances is this behaviour permissible. This behaviour is considered
to be abuse of the spectrometers and any user doing this will be subject
to having their NMR accounts locked out.
If the spectrometer
is apparently hung up and no-one from NMR staff is available to fix
the problem, please just leave the machine with a note indicating
it is hung up. Send emails and/or leave notes with NMR staff informing
us of the problem. Unfortunately it is not always possible to have
all machines running 100% of the time - this is just a fact of life
with computer-driven equipment and it is not an excuse for abusing
the spectrometers.
As background
information regarding this policy, let me offer the following. Soon
after our new DPX-400 spectrometer was installed I was running some
checks on it and it hung up. I rebooted the SGI computer and upon
doing so the 1H amplifier immediately stuck on at full power. I was
able to quickly reset the amplifier, thus preventing any damage to
the system. However, if the SGI had been rebooted and the amplifier
problem not noticed, major damage to the amplifer and the probe would
have resulted. Thus, for the safety of the equipment, I feel very
strongly that only NMR staff may reboot the computers.
Please keep
in mind that with the logging mechanisms present on the SGI computers
it is trivial to determine if an individual rebooted the computer.
2. Removal
of locking screen savers on the Bruker Avance spectrometers.
There have been
instances lately in which an NMR user ran into any other user's reservation,
but because the first user had a locking screen saver in use the second
user was not able to stop the first user's experiment and log them
out. Therefore, I have removed the locking screen savers from the
Brukers' host computers. In future, if a user has run into your reserved
time, simply halt the user's acquisition ("halt" command),
appropriately close any open lock and vt windows, exit XWinNMR and
then log the user out. It is the second user's responsibility to ensure
that the first user's experiment is stopped correctly so that no data
is lost.
3. Opening
Lock Display while the spectrometer is locking - Bruker Avance spectrometers.
I have noticed
that some users on the Bruker Avance spectrometers have developed
the habit of issuing the "lock" command and then opening
the lock window ("lockdisp") while the spectrometer is locking.
I have come to believe that this practice contributes to the problem
of the lock window occasionally not opening. From now on, please operate
in the following way:
a) open the
lock window with the "lockdisp" command prior to issuing
the "lock" command,
or,
b) wait until
the "lock" command finishes (i.e., the spectrometer establishes
lock) before opening "lockdisp".
4. Off-Line
NMR data processing
a) RRC-East
NMR lab. We recently purchased a new SGI O2 workstation (R5200) and
this has been installed in the RRC-East NMR lab along with a new laser
printer. We have purchased a license to run Bruker's XWinNMR package
on this new computer, and this software has been installed and is
now available for use. This workstation provides off-line NMR data
processing capability using the same software that is on our new Bruker
Avance NMR's, and any Avance user is automatically granted access
to this new workstation. In addition, NMR data is shared between the
new workstation and the two spectrometers so that it is not necessary
to manually move data around between the computers. Other highlights
of the new workstation include faster processing and printing than
the Avance host computers, and easy access by any user to the Jaz
drive (for data archiving).
b) Computer
Facility. A new 667-MHz Pentium-III PC has been purchased and installed
in our departmental computer facility (4114 SES). This PC is equipped
with the 2D version of NUTS, which is a third-party NMR data processing
program. This software can process 1D and 2D NMR data obtained on
any of our spectrometers. The software is easy to use and quite fast
on this PC. One important facet of this software is that it provides
the ability to cut-and-paste spectra into e.g. word-processing documents.
To facilitate this, Microsoft Office has been installed on this PC.
Another useful application of this PC is for data archiving: using
the WS-FTP software package one can copy data directories from our
Avance spectrometers to the PC where they can then be archived to
the built-in ZIP drive. Anyone who wants to use this PC should see
Dr. Dan McElheny to get a login set up.
5. Inappropriate
behaviour towards NMR Facility student assistants.
Finally, there
apparently have been a couple of instances lately when NMR users have
become unpleasant and belligerent with NMR T/A's. In my opinion there
is no excuse for this type of behaviour. The NMR T/A's work very hard
to keep our Facilities running well, and even if it happens that one
of them makes an error or mistake that is no reason to act in an unpleasant
manner towards them. Please keep your behaviour civil.
In closing,
if anyone has any questions or comments, please don't hesitate to
contact me.
October 9th, 2000
To: Faculty
and Staff
From: Dr. Dan
McElheny, Director, NMR Facilities
Re: NMR Facility
News
The purpose
of this memo is to brief everyone on what has been happening recently,
and what will be happening in the near future, with our NMR Facilities.
RRC-East
NMR Lab - upgrades and improvements
We have a few
developments to report regarding the equipment in this lab.
1. CP-MAS upgrade
(DRX-500). The CP-MAS Level-1 upgrade was installed on our DRX-500
in June of this year. This upgrade was funded by an NSF-CRIF proposal
submitted in January 1999. This installation works very nicely and
has been tested with solid samples from the Frydman group and with
supported-phase samples from the Crich group. Installation of the
CP-MAS probe takes approximately 30 minutes and the automatic spinning
regulation system is easy to use and very stable. We anticipate on
average one to two days per week solids usage on the DRX-500 as the
four faculty members who contributed to the CRIF proposal get their
projects underway.
2. BBO Z-gradient
probe (DPX-400). At the moment, of our two new NMR's, only the DRX-500
has a conventional-geometry broadband-observe 5mm probe. This type
of probe is used for direct 13C (or other X-nucleus) observation,
and this type of usage is very common with our user base. In order
to maximize the utility of our new NMR lab, I have ordered a similar
probe for our new DPX-400, to complement the current inverse-geometry
probe. This new 5mm BBO probe will be equipped with a Z-gradient coil
for gradient-enhanced 2D spectroscopy (the 5mm BBO probe on the DRX-500
was upgraded to Z-gradient capability early this year). This probe
will allow maximum flexibility in scheduling and will permit the observation
of 13C spectra at high sensitivity even when the DRX-500 is unavailable.
The inverse probe will continue to be available for the DPX-400 for
high-sensitivity 1H applications. We anticipate delivery of this new
probe by the end of the year.
Varian Mercury-Vx-300
Our Varian VXR-300S
NMR spectrometer was upgraded in May and June of this year to a new
Mercury-Vx console with a 50-sample sample-changer accessory. The
console upgrade included a new Sun Ultra-5 host computer which is
much faster than the old Sun 3/60. A new Nalorac QNP+ 5mm probe was
obtained to complement the new console and this was installed last
month, thus making the Varian effectively an all-new system. Funding
for this new equipment was provided by the Dreyfus Foundation and
the NSF CCLI A&I program, as well as UIC matching funds. I will
be sending out another memo shortly regarding the need to expand the
usage of this spectrometer in our undergraduate teaching labs.
Despite a few
minor installation glitches the new Mercury system is running very
well. The new computer is extremely fast and the console performs
very well and seems quite robust. The sample-changer hardware and
automation software have been set up and also work nicely, although
we have not yet tested the equipment with a full complement of fifty
samples. The Nalorac QNP+ probe allows for observation of any of the
four nuclei 1H, 19F, 31P and 13C without retuning the probe, with
the option of observing other X-nuclei being available after probe
retuning by NMR facility staff. Speaking of staff, Alex Bischoff deserves
a big thank-you for all of his assistance with the installation and
setup of the new Varian system.
Please keep
in mind that although the sample-changer was purchased using funding
obtained from teaching-related proposals it can be used for research
when not being used for teaching. Thus if anyone has a series of many
samples to be run back-to-back this equipment is perfectly suited
to the task.
Off-Line
NMR data processing
1. RRC-East
NMR lab. We recently purchased a new SGI O2 workstation (R5200) and
this has been installed in the RRC-East NMR lab along with a new laser
printer. We have purchased a license to run Bruker's XWinNMR package
on this new computer, and this software has been installed and is
now available for use. This workstation provides off-line NMR data
processing capability using the same software that is on our new Bruker
Avance NMR's, and any Avance user is automatically granted access
to this new workstation. In addition, NMR data is shared between the
new workstation and the two spectrometers so that it is not necessary
to manually move data around between the computers. Other highlights
of the new workstation include faster processing and printing than
the Avance host computers, and easy access by any user to the Jaz
drive (for data archiving).
2. Computer
Facility. A new 667-MHz Pentium-III PC has been purchased and installed
in our departmental computer facility (4114 SES). This PC is equipped
with the 2D version of NUTS, which is a third-party NMR data processing
program. This software can process 1D and 2D NMR data obtained on
any of our spectrometers. The software is easy to use and quite fast
on this PC. One important facet of this software is that it provides
the ability to cut-and-paste spectra into e.g. word-processing documents.
To facilitate this, Microsoft Office has been installed on this PC.
Another useful application of this PC is for data archiving: using
the WS-FTP software package one can copy data directories from our
Avance spectrometers to the PC where they can then be archived to
the built-in ZIP drive. I am very grateful to Don Rippon for his extensive
assistance in getting this PC set up.
Web-based
instrument reservation
One of our ongoing
projects has been the development of a web-based instrument time reservation
system. Recently, Devin Sears completed the adaptation of some freeware
scheduling software available from Indiana University to our Facility's
needs. We are in the final stages of testing this software. After
this, we can decide how to migrate our current instrument rime reservation
system to the on-line system. A big thank-you goes to Devin for the
huge amount of effort he has put into this project.
In closing,
if anyone has any questions or comments, please don't hesitate to
contact me.
May 9th, 2000
Dear Avance
Users,
This morning
I was able to bring our DRX-500 back on line. The limited amount of
testing I was able to do suggested that it was functioning properly.
Please consider the spectrometer to be open for use. If you experience
any problems please document them thoroughly and let me know.
What
Happened
As far as I
can tell, the disk drive in the SGI O2 computer suffered a catastrophic
failure sometime during the night of Monday May 1st. I have never
experienced such a failure, which was without warning, in all my years
of working with UNIX systems. Because such a failure is so rare, I
initially mis-diagnosed the problem as a computer board, but a second
day of diagnosis and swapping components with the DPX-400 computer
showed that the disk was at fault.
If any of you
has any information that might be relevant to the drive failure (e.g.,
a power glitch occurred), please let me know as it is important to
document such occurrences.
How
It Was Fixed
Since the exact
replacement disk is no longer available new, an exact replacement
disk and mount was ordered from a third-party vendor. This was done
because Don Rippon and I had expected that the problem with the disk
was actually on the circuit board that is part of the disk assembly.
By obtaining another disk of the same type, we hoped to swap the circuit
boards on two disk assemblies and thus "repair" the original
disk drive. This would have allowed me to get the system back up more
quickly since no system installation and configuration would have
to be done. In addition, we would have saved all of the NMR data on
the original disk.
Unfortunately,
swapping the circuit boards did not fix the problem, so the "new"
disk drive had to be installed in the 500 computer. This meant that
the operating system and NMR software also had to be installed, and
some system configurations carried out.
Ramifications
I will attempt
to get the data on the original disk recovered. Unfortunately, many
of the parameter sets on the 500 were lost. I will try to recreate
as many of them as possible. In the meantime, if you have run a specific
experiment on the 500 in the past and want to run it again, all you
have to do is to read the old data set, copy it to a new dataset (wrpa
command), and then start your experiment using the new dataset.
What
Each of You Needs to Keep in Mind
As it happened,
no user data was lost, since the user data is on the 6GB external
disk. In addition, I backed up the external disk while the 500 was
down. Unfortunately, I lost a lost of data that I had obtained for
testing purposes on the 500 during the last few months. I do not know
if it can be recovered. This just goes to show the importance of backing
up your data.
I want to stress
to every one of you that ultimately it is your responsibility that
your data is secure. I strongly recommend either:
1. copying data
to computers in your own labs, using e.g. Fetch, and then to a tape
or ZIP disk, or,
2. copying your
data to an account in our computer facility, and then to a Jaz disk,
or,
3. copying your
data directly to a Jaz disk in the NMR lab (at the moment I have to
help you with this, although this will be remedied when we obtain
a third SGI computer in the NMR lab for data processing and archiving).
In addition,
it has become apparent that some of you have way too much data
in your data directory. A couple of users have 200 and even 400 MB
- the requested limit is 100 MB. I ask all of you to please delete
(after archiving if necessary) any data that is no longer needed.
Finally, I would
like to thank Don Rippon for his help with this problem, and you NMR
users for your patience.
- Dan McElheny
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