On-Campus Users: Samples can be dropped off in RM 18 in the Chemistry and Biochemistry building at the designated sample drop-off areas. Sample tags should be filled out to indicate user, file name, experiment(s) requested and desired NMR solvent. Sample tags can be printed and filled out ahead of time by downloading and printing the appropriate pdf form for 500MHz or 600 MHz use.

Local External Users: Samples can be dropped off  at MSU in RM 18 in the Chemistry and Biochemistry building. Sample tags should be filled out to indicate user, file name, experiment(s) requested and desired NMR solvent. Sample tags can be printed and filled out ahead of time by downloading and printing the appropriate form for 500MHz or 600 MHz use.

External Users: Samples can be sent to the MSU NMR facility at the following address using an appropriate delivery service.  Montana State University, 103 Chemistry andf Biochemistry Bldg, Bozeman, MT, 59717, Atten: NMR Facility. Users must indicate if samples are to be returned.

Retrieving NMR Data from the MSU Blackmore NMR Facility server

Windows Operating System

For windows users, you need to be connected to the MSU-secure network or MSU VPN (an activated Cisco connection, see MSU web site regarding set-up) outside of campus.

Open Windows File Explorer (the folder icon) 

In the location bar type... \\blackmore.msu.montana.edu\nmr-facility-student\

Hit return and wait for credential login screen. Use your MSU net id and password. Note you are logging into the MSU domain. Add MSU\Net id for user. You can only log into the server if you have already given the facility manager your credentials. 

Migrate to the NMR data (400, 500 or 600) desired. If runs were collected using the ICON software chose the ICON folder. If runs were collected in manual mode, chose the Topspin folder and migrate to your data folder.

 

Mac Operating System

For Mac users, you need to be connected to the MSU-secure network or MSU VPN (an activated Cisco connection, see MSU web site regarding set-up) outside of the campus.

Open Finder

At the top of your screen select "Go" then "Connect to Server"

In the text feild enter smb://blackmore.msu.montana.edu/nmr-facility-student/

Hit the "+" in the lower left of the window then click "connect"

When prompted to enter your name and password, select "Registered User", enter your NetID in the Name field enter your NetID password in the Password field, and click "Connect". Note You can only log into the server if you have already given the facility manager your credentials. 

The share should now be accessible under Finder, Go, Connect to Server

Migrate to the NMR data needed (400, 500 or 600). If runs were collected using ICON software chose the ICON folder

If runs were collected in manual mode, chose the Topspin folder and migrate to your data 

Mac has implemented some security mearsures making getting to the root Topspin data folder difficult. Use the finder "Go" tab and "Go to folder" to migrate to the location /opt/topspinXXX(your version)/Data/. Create a new folder (any name) and a sub-folder called nmr. In the upper folder choose the "nmr" folder and make an alias (control-right-click) and drop this on your desktop or desired file location. Just drop files from the server into the alias folder.

In Topspin's file location section create a new data directory and choose the alias file location. Drag and drop files onto Topspin for viewing.  

 

300 MHz NMR Computer   (No server or sftp access)

Do to security issues, the 300 MHz NMR computer cannot be accessed remotely. All user collected data must be transferred either to an individuals own flash drive for future data analysis elsewhere or to one of the in-house provided flash drives, and data files up-loaded to the users box account using one of the on-line secure NMR Facility computers. In the latter case, please delete your files from the flash drive and return it back to the computer.

For personal flash drives, please re-format your drive with the name NMRLAB 

 

Linux Operating Systems

To map a Blackmore share on Linux:

Make sure you are connected to the MSU Wired Network, MSU Secure Wifi, or MSU VPN 

Install cifs client 

Ubuntu/Debian/Mint:

sudo apt install cifs-utils

CentOS/RHEL/Fedora: 

sudo dnf install cifs-utils

Create mountpoint:

sudo mkdir </path/to/folder>

Mount share

Single-user access:

sudo mount -t cifs -o username=<YourNetID>,domain=MSU,vers=3.0 //blackmore.msu.montana.edu/nmr-facility-student <mount/location>

You can only log into the server if you have already given the facility manager your credentials. 

 

User Management

The NMR facility implements the following policies.

Users of the NMR facility must abide by the following rules and policies:

  • Report all accidents in the NMR room to the facility manager. 
  • Only qualified operators can use the NMR's. Qualified Operators are persons who have received instruction and training from the NMR facility manager.
  • Only high quality NMR tubes should be used. Tubes with chipped or cracked edges constitute a safety hazard and should not be used. Tubes overheated in an oven can be sufficiently out of tolerance as to cause damage to the probes.
  • Important! Report spilled or a broken tube in the NMR immediately. The faster a spilled/broken tube can be removed, the sooner the probe and/or shim stack can be cleaned. High costs are associated along with down time if a probe must be sent out for repair or cleaning.
  • All the instruments have accounting software that maintains a chronological log of instrument use. In addition the systems have paper logbooks. Users are requested to enter their name, research group, start and finish times, nucleus, and temperature if other than ambient temperature was used. If problems are encountered, a description of the problem should be entered in this logbook. It is helpful to NMR personnel to be able to contact persons who have experienced a problem in order to know what needs to be fixed.
  • Users must abide by rules governing NMR instrument time management.

Resource Management

  • Users must abide by the rules concerning time reservations and cancellations.
  • The NMR facility reserves the right to services/access refusal at any time if it deems the actions of the users or research may harm the instrumentation in the facility or others.
  • The NMR facility manager reserves the right to prioritize runs/experiments in the case of time-sensitive services or contracted services.
  • The NMR facility manager reserves the right to refuse NMR services that it deems would/or could not be adequately compensated for by the user.

Intellectual Management

The NMR facility institutes good intellectual management practices. Users who require signed COA (confidentiality agreements) with the NMR facility must accept that all COA agreements must first be pre-approved by the intellectual property office at MSU. User(s) collected data can either be deleted up request or encrypted for security reasons and storage. Without written consent, all users’ data will not be stored past 2 year of collection.


Fixing the baseline in 1D spectra:

The standard processing command is “abs n” (automatic baseline correction with no-integration).

For 19F and 13C spectra which may still have a rolling baseline, try increasing the number of SI points and then use the processing command “apbk”.

For 15N spectra with very short fid decay data, first copy the processed spectra to 2 (wrp 2) and read that file (re 2). Then process the spectra using the command “cryoproc1d”

Frozen Lock Screen: Sometimes the lock screen can become frozen. One option to unfreeze the screen is to use the command “restart gui”.

Line vs data points: To view individual data points in a spectra ( i.e. to see the number of data points/peak) instead of line spectra, select “spectra display preferences” then “show data points”.

Load gradient files: To quickly input/load gradient files into a new bruker parameter set when setting up a new experiment. Use the command “gppp”.

HOESY experiments: For hoesy pulse program experiments, it has been suggested to use 5% gradient strength.

Shimming on non=deuterated solvents (no-D shimming):

Option-1 (Bruker)

Bruker has a supplied script for shimming of non-deuterated solvents. The command is “lctshim”. The script looks for the largest peak, set the o1p, sets selwid=0.5 and rga before initiating topshim.

 

Option-2 (Manual)

Load the experimental parameter set and choose “lock solvent = none”.

Set # scans , # dummy scans and reciver gain (ns=1;ds=0;rg=1).

Turn off lock with “locnuc off”.

Collect a scan (zg) and process spectra (ef;apk;abs n). Find the ppm of the center of the largest peak.

Shim with the command “topshim 1h lockoff o1p=(pk center ppm) selwid=0.5 convcomp”.

Reset ns and ds.

If topshim fails, add ordmax=3 (default is 5) to the above command.

 

One can write a macro (nod) to speed things up:

o1p

topshim 1h lockoff o1pget selwid=0.5 convcomp

zg

efp

When citing a core facility, please ensure that you are referencing their Research Resource Identifier (RRID) number, and funding source. Authors should reach out to the facility manager if you are unsure how to acknowledge a specific instrument. A citation example for the NMR facility is provided below:

"XXX NMR spectra were recorded at Montana State University on a XXXXXX NMR spectrometer housed in MSU's NMR Center (RRID:SCR_026334). Financial support for the NMR instruments and operations have been provided in part by the NIH SIG program (1S10RR13878 and 1S10RR026659), the National Science Foundation (NSF-MRI:DBI-1532078; NSF-MRI:CHE-2018388), the Murdock Charitable Trust Foundation (2015066:MNL), and MSU's Office of Research & Economic Development, and Graduate Education at MSU."