I have been working with Spinach's paramagnetic NMR functionalities and have some suggestions about the function ocparse.m used to import spin density from a .3d Orca output and a theoretical question about the PCS calculation.

First, a technicality regarding the handling of box extents. I have a .3d file with 80 grid points along each dimension, the X range being [-7 A, 14 A]. After the density is padded with zeroes, the following line of code calculates new extents of the box in Angstrom:

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`ext=(2*pad_factor+1)*ext;`

For my purposes, I modified the code so that the new box extents are calculated as:

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```
ext=[ext(1)-abs(ext(2)-ext(1))*pad_factor ext(2)+abs(ext(2)-ext(1))*pad_factor...
ext(3)-abs(ext(4)-ext(3))*pad_factor ext(4)+abs(ext(4)-ext(3))*pad_factor...
ext(5)-abs(ext(6)-ext(5))*pad_factor ext(6)+abs(ext(6)-ext(5))*pad_factor];
```

I also believe that the following line of code in ocparse.m

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`density=permute(density,[2 3 1]);`

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`density=permute(density,[3 2 1]);`

while using the latter works fine (positive spd located in a dxy orbital at the metal atom with delocalization to coordinated Cl- ligands):

So it seems that the original code incorrectly switches the X and Y directions. (Again, I believe that this incidentally does not produce an error for the Cu porphyrin example because the model is axially symmetric around Z).

With these issues fixed, the procedure outlined in the Cu porphyrin example finally gives reasonable pseudocontact shifts which converge with increasing pad_factor for my system, so I now look forward to playing with it more

Last, I have a question about the physics. I am curious about the link between the paramagnetic centre probability distribution the PDE operates with and spin density output from QC calculations. I noticed ocparse.m takes the absolute value of the spin density. In your opinion, would it have meaning to use the original spin density with both signs for the PCS calculation? Granted, any beta spin density is a few orders of magnitude smaller than alpha spin density, so this effect should be relatively small. Still, I would be really grateful for any insight about this last point so that I can understand the calculation better

Best regards

Petra Pikulová