Validate spectra - adjust paths


One of the nice features in v2 was the ability to move all the paths of files when you open the project from a different location, or after moving data around. I found the `Validate spectra` feature, but I am not sure that I fully understand the employed nomenclature. Is there an explainer anywhere about how that dialog works and what things like `$INSIDE` and `$ALONGSIDE` are supposed to mean/do?

Best wishes,

Hi here is my understanding for people to shoot done modify and comment on!

So VP (validate spectra or validate paths) shows you the key data paths and shortcuts for them

$DATA is the users homie directory
$INSIDE is the directory that holds the projects contents
$ALONGSIDE is the directory that contains the project directory and you can puts spectra on a relative path to it to ake moving the project around easy

So for example say my home is


and I have a project stored in



$DATA = /Users/garyt
$INSIDE = /Users/garyt/projects/abc.ccpn
$OUTSIDE = /Users/garyt/projects

Other directories with common path roots that are not contained by $INSIDE or $OUTSIDE are named remoteData<_some_number>

so if you had /Users/garyt/spectra/hsqc.spc thaty might be [remoteData]/spectra.hsqc

But /Users/garyt/projects/spectra/hsqc.spc would be $OUTSIDE/spectra/hsqc.spc

remoteData directories appear in the upper section which should allow them to be edited and changed (but note [remoteData] not sure why

In the Lower part of the dialog paths are shown which I believe can include $DATA $INSIDE etc

If the path exists and it is a recognised data file the field is green if its yellow the file / directory exists but it isn’t a valid data file and if its red it doesn’t exist

I have noticed that the dialog can be incredibly laggy and plan to investigate soon!


Hi Gary,
Thanks for the response. That kind of helps, at least enough to realise that this dialog in fact does not replace the functionality of the v2 path/directory editor function (where you could change the paths of many files at once).
Would it be possible to re-introduce this functionality? It is really important, as we are often accessing the same data from different access points (via remote mounting a shared network folder).A related question: it is starting to look to me like the new version is no longer beta, but maybe not quite operational yet. Should we stick with version 2 for now?


Hi Patrick,

V3 is now at a bit of an `in-between` stage. If you are starting a new assignment project, it works nicely and is functional and certainly beyond beta. But although V3 has some features that V2 doesn`t have (e.g. phasing), there are still many V2 features that it lacks. You can see a list of things at
So for the moment you may be better off staying with V2. I certainly know a number of people who are waiting for specific functionality before they are willing to switch.
In the mean time I`ll see what we can do about changing lots of paths at once.

Best wishes,


Hi Patrick,

worth adding that if you wanted to change lots of paths in one go, you could do it with a macro. e.g. the following would change the relative path for all your spectra:

  1. specPath = `/New/File/Path/`
  2. for spectrum in project.spectra:
  3. specFileName = spectrum.filePath.split(`/`)[-1]
  4. spectrum.filePath = specPath+specFileName

For Bruker data you would probably want to adjust the specFileName part so you don`t just keep the file name, but some of the data structure, too.

If you wanted to something for spectra individually (e.g. with copy/paste), the following might be useful:

  1. sp=project.getByPid(`SP:hsqc`)
  2. sp.filePath=(`/New/File/Path/Filename)

Best wishes,


Hi Vicky,

Thanks for the information on this script. For now it seems a bit of a moot point until we can actually import our projects. Once that works we can give it a try.