Structure using v 3.2

Analysis Version 3
#1

Hi!

I can’t seem to find a way to use TalosN or Xplor in the latest version. According to the structure tutorial pdf, there should be a “structure”-tab where one can choose to e.g. setup Xplor_NIH structure calculations, but I don’t have a “strucutre”-tab in my version of CcpNMR. I went back to a previous version (3.1.1) and couldn’t find the tab there either.
Am I missing something? I have both TalosN and Xplor installed locally on my computer.

Furthermore, in the Macro-tab, there is an option that is called CalculateSecondaryCACB. When I try to use this option I get an error window stating “ChemicalShift list not found” and that I should “Set the chemicalShiftList pid in the macro”.

Thank you for your time.

Kind regards,
Dani

#2

Hi Dani,

You need to make sure that you run AnalysisStructure, not AnalysisAssign. So you will need to start the program with the command ./bin/structure in your Analysis directory or by double-clicking structure.bat - depending on your operating system.

What you need to do for the macro, is to open the macro in the Macro Editor (go to Macro / Open CCPN Macro… and then select it). Then in line 57 you will need to specify what your ChemicalShiftList is called. You can copy from the sidebar using the right mouse menu if you like:

Screenshot 2023-09-05 at 09.40.24

and then paste into the Macro Editor with Ctrl+V.

Vicky

#3

Thank you very much, appreciate the fast help!

Kind regards,
Dani

#4

Thank you for your quick reply!

I have a another, very basic question regarding the shift perturbation analysis in v3: Why isn’t the protein concentration considered when setting up the calculations (or do I have to use Equivalents rather than molar units when I set up the spectrum group)?

Kind regards,

Dani

#5

You don’t have to use equivalents. But it basically all depends on what equation you want to use. I’m actually hoping that by the end of the week I’m going to be able to start putting together some documentation on all of this and adding in new equations.

Vicky

#6

Ok I see, thank you again.

Dani