[Biopython] Variation in distance calculation between Bio.PDB and PyMol

[Peter Cock]

Hello Salma,

Have you computed that example between MN1 and the O1
ligand "by hand" from the PBD file to get a tie breaker?

Brainstorming about other possible sources of discrepancy:

I would also check you are comparing the same atoms
(i.e. is the 2.4 Angstrom threshold giving the same set), in
case sometimes an atom is at/on the boundary?

Are you looking at NMR structures with multiple models? if
so are both scripts looking at the same model or models?

Peter



On Tue, Feb 27, 2024 at 8:50 PM Salma Yahia <salmayahia995 at gmail.com> wrote:

> Dear Sir/Madam,
>
> I hope all is well. I am asking about a problem when analyzing a specific
> structure using the Bio.PDB module. I am trying to calculate the distance
> between the manganese atom(Mn) and the surrounding ligands within a 2.4Ă
> radius (for oxygen-evolving complex OEX) in the photosystem II (PSII)
> protein complex, then calculate the average distance for all the resulting
> distances.
> The problem is that the calculated average distance is less than expected,
> so I checked the distance between MN-Ligands of the OEX complex using
> PyMol. I found that 90% of the distance calculated in the code is always
> less than what’s in PyMol.
> For example, if the distance in the code Between MN1 and O1 ( ligand) is
> 1.75, it is 1.8 in PyMol, and sometimes the variation is wider than just
> 0.05!
>
> So, what might cause this variation between PyMol and the code using
> Bio.PDB and this is not happening for only 1 PDB file; this problem is with
> 10 different PDB files!
>
> Any useful insights from you would be appreciated; I am attaching my code
> for more clarification. Thank you for your time and consideration. I am
> looking forward to hearing from you soon.
>
> Warm regards,
> Salma Yehia
>
>
>
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