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

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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 2.4=C4=
=82
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=E2=80=99s 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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<div dir=3D"ltr"><span style=3D"font-family:Calibri,sans-serif;font-size:14=
.6667px">Dear Sir/Madam,</span><br style=3D"font-family:Calibri,sans-serif;=
font-size:14.6667px"><br style=3D"font-family:Calibri,sans-serif;font-size:=
14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-size:14.6667p=
x">I hope all is well. I am asking about a problem when analyzing a specifi=
c structure using the Bio.PDB module. I am trying to calculate the distance=
 between the manganese atom(Mn) and the surrounding ligands within a 2.4=C4=
=82 radius (for oxygen-evolving complex OEX) in the photosystem II (PSII) p=
rotein complex, then calculate the average distance for all the resulting d=
istances.</span><br style=3D"font-family:Calibri,sans-serif;font-size:14.66=
67px"><span style=3D"font-family:Calibri,sans-serif;font-size:14.6667px">Th=
e 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=E2=80=99s in PyMol.</span><br style=3D"font-family:Calibri,sans-serif=
;font-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-si=
ze:14.6667px">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!</span><br style=3D"font-family:Calibri,sans-serif;font-size=
:14.6667px"><br style=3D"font-family:Calibri,sans-serif;font-size:14.6667px=
"><span style=3D"font-family:Calibri,sans-serif;font-size:14.6667px">So, wh=
at 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 differen=
t PDB files!=C2=A0</span><br style=3D"font-family:Calibri,sans-serif;font-s=
ize:14.6667px"><br style=3D"font-family:Calibri,sans-serif;font-size:14.666=
7px"><span style=3D"font-family:Calibri,sans-serif;font-size:14.6667px">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.</span><br style=3D"font-family:Calibri,s=
ans-serif;font-size:14.6667px"><br style=3D"font-family:Calibri,sans-serif;=
font-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-siz=
e:14.6667px">Warm regards,</span><br style=3D"font-family:Calibri,sans-seri=
f;font-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-s=
ize:14.6667px">Salma Yehia</span><br><br><br><br><img width=3D"0" height=3D=
"0" class=3D"mailtrack-img" alt=3D"" style=3D"display:flex" src=3D"https://=
mailtrack.io/trace/mail/e44d634a26d9e0d2de7011c4bdf74dd57bde7a3a.png?u=3D10=
005938"></div>

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