NMR INSTRUMENTS AT NYSBC:
The NYSBC NMR instrumentation available for use are: http://nysbc.org/departments/nmr/instrumentation/
The sensitivity of the NYSBC NMR instruments is listed at: http://nysbc.org/departments/nmr/instrumentation/probes/
NYSBC Instrument Schedule: http://www.nysbc.net/twiki/bin/view/Main/NmrSchedule
NYSBC Solids Probes Status: http://www.nysbc.net/twiki/bin/view/Main/SolidsProbestatus
Einstein Slots at NYSBC: Einstein & Open Slots at NYSBC
NEED NYSBC ACCOUNT:
If you are not an NYSBC user yet but wish to have access to the NMR instruments there, please let Sean Cahill (EinsteinNMR Contact Info) know and we will start the process of getting you an NYSBC account (see "How to become an NYSBC Affiliate" under https://nysbc.org/departments/nmr/nmr-access/)
Also register as a user on the NYSBC intranet to get access to the NYSBC Intranet web: http://www.nysbc.net/twiki/register.html
NOTE:
Registration as a user on the NYSBC intranet does not affiliate you at NYSBC, it only allows you to access to the NYSBC Intranet web at http://www.nysbc.net
SCHEDULING NYSBC TIME:
If you need time on the NYSBC NMR instruments, please check the following: Einstein & Open Slots at NYSBC
Any Einstein slot with “USER” is unassigned. Please let Sean Cahill (EinsteinNMR Contact Info) know if you would like to reserve any of the unassigned Einstein slots or OPEN slots.
NOTE:
If a user’s slot is listed as “TENTATIVE”, let us know if you would like to be listed as standby and we will contact you if the slot becomes available.
For all NYSBC slots, see http://www.nysbc.net/twiki/bin/view/Main/NmrSchedule
NYSBC summary page for Einstein (updated weekly by NYSBC): see http://www.nysbc.net/library/Einsteinweek.html
NYSBC NMR USER ACCOUNT AND DATA INFO:
Once you become an NYSBC affiliate, you will get a username/password to log into the NMR instruments (NOTE: these will not be the same as your username/password for the NYSBC intranet (nysbc.net)).
Your home directory will be located in: /opt/topspin/data/'your username'/home
Your datasets should be located in: /opt/topspin/data/'your username'/nmr
NOTE! Please make sure you create datasets in your assigned data directory - if your datasets are not in this location, they might not be backed up to the data server and might not be available for download to your computer!!
Every user on each instrument has their own "stan" directory (in /opt/topspin/exp/stan.'your username') that will contain all the standard Bruker pulse sequences and parameter sets as well as any that you need to create or modify (those are stored under "user" in the appropriate directories)
NEED HELP SETTING UP NMR EXPERIMENTS AT NYSBC OR HAVE ISSUES WITH THE NMR INSTRUMENT DURING USE:
Slots on the NMR Instruments usually START on Tuesdays at 12noon and END the following Tuesday before 9am so that magnet fills and instrument maintenance can be performed (see "NYSBC Consortium Scheduling" under https://nysbc.org/departments/nmr/nmr-access/)
For help or issues with the NMR instrument, please contact (it is best to send an email to everyone below to get fastest response):
Sean Cahill: EinsteinNMR Contact Info
NYSBC staff: nysbc.org/nmr-personnel/
Mike Goger, Ph.D. (NMR Manager): http://www.nysbc.net/twiki/bin/view/Main/MichaelGoger
Shibani Bhattacharya, Ph.D. (Solution NMR): www.nysbc.net/twiki/bin/view/Main/ShibaniBhattacharya
NOTES:
if you need advice or help with setting up NMR experiments, please contact us at least a day or more in advance of your assigned slot to make sure someone is available to assist you.
NMR SAMPLES AT NYSBC:
since a lot of samples end up in fridge at NYSBC and you might end up with a few more yourself, it is recommended to put at least a unique ID on each one such as a date and lab notebook number or sample ID and also labeling scheme/solvent such as 13C/15N in H2O, etc.
Make sure to put sample ID on BOTH the tube carrier AND the NMR tube. The tube carrier should also contain your name and contact info.
Also, put a note on keyboard with instructions on what to do with NMR tube when it is removed from magnet such as "please put nmr tube in the tube carrier near the keyboard and store in NYSBC fridge". The note should also contain your name and contact info.
PUTTING NMR SAMPLES INTO INSTRUMENTS AT NYSBC:
If your sample is already stored at NYSBC and you need assistance to put it in the NMR instrument, you might be able to get help from NYSBC staff (see above section for contact info). Please contact them at least a couple of days in advance of your run to confirm that someone is available. Let them know the following so they can properly set-up sample for you:
where the sample is located and what is the sample ID
sample temperature needed for NMR experiments
lock solvent (for example 100% D2O or 90% H2O/10% D2O)
isotope labelling used and what nuclei are needed for your NMR experiments
Also, make sure you give instructions on what to do with NMR sample when it is removed from magnet after your slot is completed.
If no one is available, you will need to make arrangements to put the sample in yourself and take the sample out.
NEED REMOTE ACCESS TO NYSBC NMR INSTRUMENTS:
Contact Sean Cahill (EinsteinNMR Contact Info) who will submit a remote access request (http://www.nysbc.net/twiki/bin/view/Main/NmrRemoteoperation). Please contact at least a day before you need a remote connection.
Also, please provide the IP address of the computer you are connecting from (for example, by using whatismyip.com).
NOTES:
With CentOS and real VNC for remote access will get a blank screen unless you are logged in - make sure the you are logged into the desktop before connecting (or get NYSBC staff to log in for you)
assume that the remote access connection will only work between 9am and 5pm Mon-Fri so make sure to set-up all of your experiments during that window. Also, remote connections at the start of the slot will generally be turned on once the instrument becomes available which is at 12noon on Tuesdays.
SFTP DATA SERVER:
data and experiment libraries and backed up to sftp server frequently - use the sftp server to either retrieve your data or upload files to the spectrometers.
SFTP INFO: http://www.nysbc.net/INFOTECH/sftp.html
Data directories and pulse sequences and parameter sets for each instrument can be found under /nysbc_nmr
Data can be found under: /nysbc_nmr/'instrument name'/topspin/data/'your username'/nmr
Pulse sequences and parameter sets can be found under: /nysbc_nmr/'instrument name'/topspin/exp/stan.'your username'
NOTES:
YOUR DATA WILL ONLY GET BACKED UP TO THE SFTP SERVER IF IT IS LOCATED IN THE CORRECT DATA DIRECTORY of the instrument - please make sure your datasets are located in: /opt/topspin/data/'your username'/nmr !!!
The SFTP SERVER will be unavailable for maintenance every Monday between 10 am and 2pm. The system may appear to be on-line during this period, but attempted transfers may fail.
DATA LIFETIME ON NMR INSTRUMENTS AND SFTP SERVER:
ser data files are removed after 90 days on the NMR instruments and the SFTP server. Fid files and the acquisition and processing parameters are not removed.
Please transfer data that is collected at the NYSBC to local machines as soon as possible to avoid loss of data
ISSUES WITH NMR INSTRUMENT COMPUTERS OR ACCESSING NMR DATA REMOTELY:
Contact NYSBC InfoTech: http://www.nysbc.net/INFOTECH/contactus.html
NOTE! please CC Sean Cahill, Mike Goger and Shibani Bhattacharya on any email sent to InfoTech so that we are aware of the issue.
InfoTech FAQ: http://www.nysbc.net/INFOTECH/faq.html