VideoTutorials
& Manual
My Mac says "macOS cannot verify the developer... Are you sure you want to open it?". What can I do?
The program won't run on my M1/M2 Mac. What can I do?
The program won't run on my Windows computer. What can I do?
Can I use CcpNmr Analysis remotely?
What data types can I load?
My project won't open - what should I do?
Can I synchronise axes across my SpectrumDisplays?
Why can't I see the coloured Peak Assignment lines in my SequenceGraph?
How can I get a molecule from ChemBuild into CcpNmr Analysis V3?
Can I use CcpNmr Analysis to analyse my peptide spectra?
Can I use CcpNmr Analysis to analyse my RNA data?
What has happened to my favourite Version 2 features?
Should I switch from Version 2 to Version 3?
Can I open Version 2 projects in Version 3?
Can I open Version 3 projects in Version 2?
Until we are able to build the software as official Apple Developers (we have been fighting this admin battle for around 3 years now!), the executables will have to be removed from ‘quarantine’ before you can use them on the newer MacOS versions. After extracting the compressed file, please run the following command in the directory where you have placed the ccpnmr3.2.0 directory:
sudo xattr -rd com.apple.quarantine ccpnmr3.2.0
and enter your password. You may see some xattr errors coming up, but these are on the whole nothing to worry about.
Alternatively, disable the Gatekeeper by typing:
sudo spctl –master-disable
and enter your password. You should then be able to run Analysis without problems.
The current version for Mac is compiled on an Intel Mac and runs on Macs with M1 and M2 chips in compatibility mode. On some computers this is not automatically enabled and you will get an error saying “Bad CPU type in executable”. If this is the case you will need to manually install the Rosetta program (nothing to do with the Rosetta modelling program!) with the following command in a terminal:
/usr/sbin/softwareupdate –install-rosetta
If you have any other issues, please do get in touch with us at support@ccpn.ac.uk.
The most common reason for our program not running on Windows is that an anti-virus program such as Windows Defender has placed some of the files in quarantine. Sometimes this results in missing files e.g. in the ccpnmr3.x.y/miniconda/Lib/site-packages subfolders (in particular the h5py folder) or files which are 0kB in size. The best things is to contact your IT support and find out how to mark your ccpnmr3.x.y folder as being safe. How to do this will obviously vary from one anti-virus program to another.
Another thing to watch out for is that the download .zip file has been properly unzipped. On Windows it often looks as though the folder has been extracted when in fact it hasn't.
Yes and no. We strongly recommend that you have your project on a local disk. This is because Analysis regularly writes to your project files and is currently not set up to deal with temporary breaks in the connection. You could therefore easily end up with your project in a compromised state which will later make it unreadable. However, if your spectrum files (which are generally what takes up lots of disk space) are on a remote disk/server, then that is fine. Analysis only has to read these files and so there shouldn't be any issues.
Finally, you can of course also log into a different machine through VNC Viewer (e.g. to NMRBox), TeamViewer or some other such package and work on a remote workstation. In this case, it is simply the graphics which are being relayed back to your local computer. The important thing is that your project is stored on the same computer on which are running CcpNmr Analysis.
CcpNmr Analysis can read the following types of files:
Bruker data: in order to open Bruker data correctly, Analysis needs to be able to read several files and not just the 1r/2rr/3rrr/.../8rrrrrrrr file (please do not rename these files!). You can drag and drop the 1r/2rr/3rrr file (or the procs file) into Analysis to open the spectrum, but they must be contained within the Bruker file structure so that Analysis can access the other files it needs to read and display the data correctly.
.dat, .fid, .ft1, .ft2, .f3 or .ft4: read in as an NmrPipe processed Spectrum
.ucsf: read in as a ucsf format Spectrum
.spc with .par: read in as an Azara processed spectrum. Both files must be present, but either can be dragged and dropped or selected.
.dat or .mat: read in as a Felix processed Spectrum
.ndf5 or .hdf5: read in as an Hdf5 format Spectrum
.nv: read in an NmrView format Spectrum
.param or .16: read in as an Xeasy format Spectrum
.dx or .DX: read in as a JCAMP format Spectrum (currently only works for 1D spectra)
.save: read in as a Sparky format saved Spectrum
.proj: read in as a Sparky project
.nef: read in as an NMR Exchange format file. Can be either used to open a new project or imported to the current project.
.str: read in as an BMRB NmrStar file, but currently only loads the assignments as a ChemicalShiftList and NmrChain. Can be either used to open a new project or imported to the current project.
.fasta: read in as a new Chain
.pdb: read in as a StructureEnsemble
.py: read in as a Macro
.xlsx: if correctly formatted, then this can be used to read in many Spectra as well as other Screening related data (Substances and their properties etc.)
folder.ccpn: a folder with .ccpn will be opened as a CCPN project
folder: the program will check whether this is a V2 project folder or a folder from a Bruker file tree, alternatively if it contains any other types of files that can be loaded (spectrum, sequence, structure, text etc.), then all of these will be loaded.
First of all, it may be worth seeing if you can restore a backed up version of your project. Have a look at our Backups page and video to find out more about how to do this. If your backups are also broken (which does sometimes happen), then the best thing is to send us the project at support@ccpn.ac.uk. We can almost always recover it in some way. By sending us the project, you often enable us to identify bugs which have caused the corrupted project and which we can then fix.
Yes, you can! We have implemented this as a macro which can link any x and y axes (but not z axes). Have a look at our Synchronising Axes page to find out how to use this feature.
In order to see these lines you will need to go to your SpectrumPreferences (double-click on a Spectrum in the sidebar) and in the Dimensions tab you will need to select the Reference Experiment Type and then set the Reference Experiment Dimensions. Once this is done, you should see the coloured lines indicating the Peak Assignments in the Sequence Graph module (as long as this has been selected in the Settings panel).
If you want to add a non-canonical amino acid to a Chain in your CcpNmr Analysis project, then you should follow our instructions on Creating non-canonical amino acid ChemComp files and Creating Chains with non-canonical amino acids.
Essentially you need to follow the same instructions to those on our Creating non-canonical amino acid ChemComp files and Creating Chains with non-canonical amino acids pages. You will need to export your ChemBuild molecule as a ChemComp file, then import it to CcpNmr Analysis and then you can create a Chain from that. You simply need to make sure that when you save your ChemComp file in ChemBuild, you select your Molecule Type to be other. And when you create your Chain in CcpNmr Analysis you also need to make sure that your Molecule Type is set to be other.
Note that it is also possible to add SMILES notations (not files) to Analysis in the Substances section:
Note that pdb files can also be dragged into a project, and will then go into the Structural Ensemble part of the data structure (note that currently only ATOM and not HETATM lines are recognised/read in). Once a pdb file has been read in, there is not much you can do with it, though. ChemBuild will allow you to import a pdb file and then export it as a ChemComop file.
Yes, of course. We are actually currently working on some new features which will help those working with peptides and we hope to create a tutorial for peptide assignment in the near future.
Yes, of course. You can easily add RNA and DNA chains to your project. Although we don't have any features which are particularly geared towards those working with RNA/DNA spectra, you can visualise, navigate and assign your spectra as you would in any other spectral assignment program. We do hope to add some RNA specific functionality and a tutorial at some point.
Have a look at our Popular V2 Features in V3 page for a list of V2 features and how they have been implemented in V3. You may also be interested in our V2 to V3 translation page which gives a direct translation of V2 mouse and keyboard commands to the new V3 commands.
Yes! Overall, V3 is a nicer, more flexible and more user-friendly programme than V2.4, as illustrated in our Switching to CcpNmr Analysis V3 talk from our 2019 conference. However, there are still a few features which haven't yet been ported from V2.4. Our Popular V2 Features in V3 page will give you a bit of an idea of whether there are elements of V2.4 that are not yet present in V3 and that you don't want to do without. The main thing to be aware of with Version 2 is that we will stop supporting it from 2025 onwards. This means no bug fixes or lengthy investigations on our part if you can't get something to work. We will also stop creating new builds for new operating systems etc. You will still be able to continue to download and use the program, though, and if you wish, you can compile the source code yourself.
Yes! This is very easy - Version 2 projects can be opened directly in Version 3. See our Importing V2 Projects tutorial on how to do this. The only caveat is if your V2 project uses labelling schemes, then at the moment you will have to do a small work-around shown in this video.
Yes, but with some caveats. You will need to save the Version 3 project as a NEF file: go to File / Export / NEF File or type EX and save everything with CCPN tags. You can then import the NEF file into Version 2.5 (not 2.4!) by going to Project / Load NEF.
Please be aware that this process is not foolproof as Version 3 contains features not contained in Version 2. In particular, you are likely to encounter problems if your project contains molecules that are not simply proteins made up of natural amino acids. Similarly, labelling is handled very differently, and any explicit labelling of molecules in Version 3 may cause problems when going back to Version 2.