View source for Rdm:nmr-bruker

== Retrieving an  NMR data file from the Bruker  Spectrometers ==
#[[Image:Jeol9.jpg|right|300px|step 3]]On Windows 10,  from the  Software Hub panel, firstly select a '''chemistry''' filter
##If you cannot see anything relating to the software hub, open a Web Browser and type: '''https://softwarehub.imperial.ac.uk/login'''  as the URL and proceed to log in using your Imperial Credentials.
##[[Image:Jeol6.jpg|right|300px|step 4]]From the list of chemistry programs (33) invoke '''MestreNova'''. Use the latest version (14).
###'''OPTIONAL''': As an alternative to Mnova, a brand new NMR analysis tool has recently appeared: https://www.nmrium.org/  In many ways this is simpler than using MestreNova but achieves the same result.  Give it a go and let us know if you prefer it to  Mnova!
#On Windows 10, type '''run''' into the search box at the bottom left.
##[[Image:Bruker1.jpg|right|300px|step 2a]]In the run box, type (or copy/paste)<br />'''\\ch-nmrserv2.ch.ic.ac.uk\Av400D\ug1\nmr'''<br /> and navigate down through to the folder allocated to your spectrum.
##If this server does not respond, try instead one of <br />'''\\icnfs3.cc.ic.ac.uk\ch-nmr\Av400D\ug1\nmr'''<br />'''\\ch-nmrserv3.ch.ic.ac.uk\Av400D\ug1\nmr''' 
#On MacOS, invoke '''Go/Connect to server''' from the Finder menus at the top and type e.g.  '''smb://icnfs3.cc.ic.ac.uk/ch-nmr/Av400D/ug1/nmr''' or '''smb://ch-nmrserv2.ch.ic.ac.uk/Av400D/ug1/nmr''' (followed by your College username and password)
##You might find it useful to drag the '''nmr''' folder that appears as a result of the above into your Finder favourites toolbar so that you do not have to repeat the above.
#The location of your file is shown on the submission sheet for your week in [https://bb.imperial.ac.uk/  Blackboard].
##[[Image:Server1.jpg|right|300px|step 4a]]Alternatively, you can find your file from the date (week) submitted and by inspection of your initials associated with a spectrum (located in the top left of the spectrum, along with the date).
##[[Image:Server2.jpg|right|300px|step 4a]]A way of checking your spectrum is to ''drag-n-drop'' a prospective folder (with a name such as '''10''' and with the correct date and initials) into the '''MestreNova''' window. 
##[[Image:Server3.jpg|right|300px|step 4a]]A spectrum will appear and initials will be shown in the top left of the spectrum. Continue until you find a spectrum with your initials. '''DO NOT''' copy a spectrum that is not yours!
#[[Image:Bruker2.jpg|right|300px|step 2b]]Once you have found your folder, select that folder,''' right click''' to get the menu shown, from which you invoke '''Send To''' and then  '''Compressed (zipped) folder'''. It will ask you ''Do you want it to be placed on the desktop itself?''  to which you reply '''Yes'''.
#*Mac users should right-click on the folder and invoke '''Compress'''.  This produces the required '''.zip''' file.
#You can next ''drag-n-drop'' the Bruker  .'''zip''' data file from the Desktop or other location into the MestreNova  window.
#[[Image:Jeol7.jpg|right|300px|step 5]]A spectrum will (again) appear. Check again it has your initials associated with it.
#[[Image:Jeol8.jpg|right|300px|step65]]When you have finished inspecting the spectrum, save the data file using '''Save as''' in three forms. Take care to note where you are saving the files (on the desktop in this example). 
##an  '''.mnova''' document,
##a '''.jdx''' (JCAMP-DX document)
##a '''.pdf''' (Acrobat document). 
#You will now have '''FIVE''' files you need to make your data deposition. These are:
##a '''.zip''' file,
##an '''.mnova''' document
##a '''.jdx''' file
##a '''.cdxml'''  chemdraw document you prepared earlier
##a '''.pdf''' file.
----
=== Crib sheet for Processing a spectrum using MestreNova ===

These are some short hints for how to quickly get the most out of your data. We assume you are analysing a proton spectrum. 
# Once you have opened the  NMR folder using  MNova, make sure the tab along the top of the program is showing '''NMR/Analysis'''
# Go to '''Chemdraw''', select the structure of your molecule and copy it/paste it into the  Mnova Window. This will serve to remind you of the molecule
# From '''1H Spectrum''' in the second row of icons, select '''compound peaks'''.  This will attempt to remove well known solvent peaks such as  CHCl<sub>3</sub> or H<sub>2</sub>O from your spectrum, which may help with subsequent integrations. You can also show only the '''solvents/Impurities''' peaks for information.
# Using the toolbar on the right of the program, find the '''Increase intensity''' icon to make the spectrum higher
# Using the toolbar on the right of the program, select the '''zoom in''' icon at the top and drag from the leftmost peak to the rightmost peak to expand the spectrum.
# In the  top '''NMR/Analysis''' icon collection, click on '''Manual integrate''' and select the left and right edges of a peak that you think you can identify. For example, an aromatic group or a methyl group.
# A (green)  integral curve will appear and below the peak a numerical integration of  '''1.00'''  will appear.
# Place the cursor on the horizontal green line just above the numeric integration.  Both the number and the integration curve go red. Now right click whilst the red is still showing.
# Select '''Edit integral''' and '''normalize''' to what you think the integral should correspond to.  Thus methyl  = 3, a monosubstituted  phenyl = 5,  a methylene group = 2 etc.
# Optionally, select '''linear correction''' and then  '''autocorrect'''.  This might improve the baseline and hence the integration.
# You can now inspect the closest integer for each peak. ''This will only be approximate''.  It will also give the total integration which  should ~correspond to the number of protons in your molecule. Obviously if your compound is a mixture of several molecules, you might not get integers for the peaks!  But you can try to get integers if you identify all the peaks due to just one molecule.
# At this stage you should save what you have obtained as a '''.mnova''' file
# Only if you are keen, select the next tab in '''NMR/Assignments'''.  You can now select a peak and assign it to a proton on the chemdraw diagram.  Save the file again.
Return to [[Rdm:synthesis-lab|Overview of files needed]] | Onwards to [[Rdm:nmr-publishing|Publishing data files]]