ChemWiki - User contributions [en]

Orcid

2026-02-24T16:28:10Z

Rzepa: /* Using your ORCID to publish research data (stage 2) */

= Signing up for an ORCID (Stage 1) =

[[Image:orcid2021a.jpg|right|300px|step 1]]Having an ORCID ('''O'''pen '''R'''esearcher and '''C'''ollaborator''' Id'''entifier) is increasingly essential for many tasks associated with researcher activities. It solves the problem of using your initials and name, which are not guaranted to be unique, especially on a global stage. Getting an ORCID is something you will only need to do once in your career, although you should strive to keep it up to date as your career develops. The ORCID system will keep some aspects automatically up to date such as your journal and data publications. ORCID is also used for some IT services on campus, such as the research data repository. The notes here will illustrate the process of acquiring an ORCID followed immediately by using the research data repository for publishing research data.
#[[Image:orcid2021b.jpg|right|200px|step 2]]Go to the site [https://orcid.org/institutional-signin https://orcid.org/institutional-signin] and start typing ''' Imperial College London'''
#Enter the username (do '''not''' add @ic.ac.uk to it on this occasion) and password for your Imperial College account and press login.
##[[Image:visibility1.jpg|right|200px|step 3]]Enter the requested details, including your Imperial College email as the '''Primary''' one and if you wish a second email to help with any future password recovery should you need it. The password field marked with a purple arrow is your '''ORCID''' password, which should be different from your Imperial College one and would be used only if you no longer have access to an Imperial College account (such as when you leave the College).
##[[Image:visibility2.jpg|right|200px|step 3]]Ensure you tick the '''Everyone''' visibility button to allow your works to be seen by everyone. Read the privacy policy and terms and conditions and finish by pressing the '''Register''' button.
#[[Image:Orcid5.jpg|right|250px|step 4]]An email will have been sent to your primary account to which you should respond to complete your registration.
#Your new ORCID takes the form https://orcid.org/0000-1234-2345-3456 (with different numbers obviously) which you should record and store somewhere safe. It will be the number you will quote in many future researcher contexts. You can also enter more details about yourself, but this is not essential at this time.
#Double check the visibility of your '''research record'''. If you want others to see it, then pull down the menu associated with your name, go to '''account settings''' and there select '''visibility settings''' and ensure it is set to '''Everyone'''. It might take an hour or so for your new research publication to appear!

If you are doing the first year course on Synthesis, go back to [https://bb.imperial.ac.uk/webapps/blackboard/content/listContentEditable.jsp?content_id=_2416994_1&course_id=_28876_1 Blackboard page].

=Using your ORCID to publish research data (stage 2) =

Research data repositories have become very common in the last few years as places where research data can be formally '''published'''. This publication process is a little different from the traditional publication in a journal, since it is not peer reviewed in the normal manner. You will be using the Imperial College repository, where the contents will be clearly associated with the identity of its publisher and therefore you will be held accountable for these contents. Furthermore, an internal check is made for each publication in this repository for suitability before it can be released to the world. You will therefore have to '''set up the repository''' in this second stage before you can use it by associating your login there with your newly set up ORCID account. To do this, proceed as follows:

#[[Image:Orcid6.jpg|right|300px|step 5]]Enter the site [https://data.hpc.imperial.ac.uk data.hpc.imperial.ac.uk] and click on '''Login'''
#[[Image:Orcid7.jpg|right|300px|step 6]]Enter your login in the form '''username@ic.ac.uk''' (the same as used for email). In the image on the right the '''username''' replaces the red rectangle.
#[[Image:Orcid8.jpg|right|300px|step 7]]Enter your College (i.e. '''NOT''' the ORCID) password and press '''Sign in'''
#[[Image:Orcid9.jpg|right|300px|step 8]]Do not stay signed in (unless you are using a personal machine)
##You may find that you are automatically logged in and do not need to action steps 2-4 above.
#[[Image:Orcid10.jpg|right|300px|step 9]]You will find yourself back at ORCID. As before, go through an '''Institutional login'''
#[[Image:Orcid11.jpg|right|300px|step 10]]When prompted enter your Imperial College login credentials.
##If you performed stage 1 just before this stage, you may still be logged into ORCID and so the step above will not be needed.
#[[Image:Orcid12.jpg|right|300px|step 11]]ORCID is now asking if the Imperial College repository can have access to your ORCID record. It needs this to record your ''data publications'' there. '''AUTHORIZE''' it.
#[[Image:Orcid13.jpg|right|300px|step 12]]You are now automatically returned to the Imperial College repository page, ready to make your [[rdm:synthesis-lab|first data publication.]]
#The next time you use the repository you may have to repeat only steps 1-3 of the above, or even just step 1.

An explanation of the data publishing process will be given on a [[rdm:synthesis-lab|separate page]]. This process results in a DOI (Digital Object Identifier) being granted in exchange for a published object (be it article, data, software etc). You can use these DOIs as citations in many different contexts.

----

On to the final three stages, [[rdm:synthesis-lab|instructions on how to publish a specific type of chemical data obtained from an NMR Spectrometer]]. Many other kinds of data can be published.

----

This page itself has a DOI taking the form '''<nowiki>https://doi.org/identifier</nowiki>''', or specifically {{DOI|qspr}}

Rzepa:

It:zscaler

2023-01-18T07:28:22Z

Rzepa: /* MaOS Interface */

2022-11-20T08:47:26Z

Rzepa: /* Retrieving an NMR data file from the Bruker Spectrometers */

== 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 (23) invoke '''MestreNova'''. Use the latest version ('''14.3''') and '''NOT''' earlier versions.
###'''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) '''\\icnfs-chnmr-backups.cc.ic.ac.uk\ch-nmr\Av400D\ug1\nmr ''' and navigate down through to the folder allocated to your spectrum.
##If this server does not respond, try instead '''\\icnfs3.cc.ic.ac.uk\ch-nmr\Av400D\ug1\nmr'''
#On MacOS, invoke '''Go/Connect to server''' from the Finder menus at the top and type e.g. '''smb://icnfs-chnmr-backups.cc.ic.ac.uk/ch-nmr/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 (or '''.jdf''' if a Jeol machine was used)
##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 CHCl3 or H2O 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]]

Rdm:nmr-bruker

2022-11-20T08:44:03Z

Rzepa: /* Retrieving an NMR data file from the Bruker Spectrometers */

== 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 (23) invoke '''MestreNova'''. Use the latest version ('''14.3''') and '''NOT''' earlier versions.
###'''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) '''\\icnfs-chnmr-backups.cc.ic.ac.uk\ch-nmr\Av400D\ug1\nmr ''' and navigate down through to the folder allocated to your spectrum.
##If this server does not respond, try instead '''\\ch-nmrserv10.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://icnfs-chnmr-backups.cc.ic.ac.uk/ch-nmr/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 (or '''.jdf''' if a Jeol machine was used)
##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 CHCl3 or H2O 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]]

Rdm:nmr-bruker

2022-11-20T07:56:48Z

Rzepa: /* Retrieving an NMR data file from the Bruker Spectrometers */

== 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 (23) invoke '''MestreNova'''. Use the latest version ('''14.3''') and '''NOT''' earlier versions.
###'''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) '''\\icnfs-chnmr-backups.cc.ic.ac.uk\Av400D\ug1\nmr''' and navigate down through to the folder allocated to your spectrum.
##If this server does not respond, try instead '''\\ch-nmrserv10.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://icnfs-chnmr-backups.cc.ic.ac.uk/Av400D/ug1/nmr''' or '''smb://icnfs3.cc.ic.ac.uk/ch-nmr/Av400D/ug1/nmr''' or '''smb://ch-nmrserv10.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 (or '''.jdf''' if a Jeol machine was used)
##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 CHCl3 or H2O 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]]