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

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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=E2=80=AFPM Salma Yahia <[email protected]=
m> 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 2.4=
=C4=82
> radius (for oxygen-evolving complex OEX) in the photosystem II (PSII)
> protein complex, then calculate the average distance for all the resultin=
g
> 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 wi=
th
> 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
>
>
>
> _______________________________________________
> Biopython mailing list  -  [email protected]
> https://mailman.open-bio.org/mailman/listinfo/biopython
>

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<div dir=3D"ltr"><div>Hello Salma,</div><div><br></div><div>Have you comput=
ed that example between MN1 and the O1</div><div>ligand &quot;by hand&quot;=
 from the PBD file to get a tie breaker?<br></div><div><br></div><div>Brain=
storming about other possible sources of discrepancy:<br></div><div><br></d=
iv><div>I would also check you are comparing the same atoms</div><div>(i.e.=
 is the 2.4 Angstrom threshold giving the same set), in</div><div>case some=
times an atom is at/on the boundary?<br></div><div><br></div><div>Are you l=
ooking at NMR structures with multiple models? if</div><div>so are both scr=
ipts looking at the same model or models?<br></div><div></div><br><div>Pete=
r<br></div><div><br></div><div><br></div></div><br><div class=3D"gmail_quot=
e"><div dir=3D"ltr" class=3D"gmail_attr">On Tue, Feb 27, 2024 at 8:50=E2=80=
=AFPM Salma Yahia &lt;<a href=3D"mailto:[email protected]">salmayahia=
[email protected]</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" sty=
le=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);paddi=
ng-left:1ex"><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:Calibr=
i,sans-serif;font-size:14.6667px"><br style=3D"font-family:Calibri,sans-ser=
if;font-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-=
size:14.6667px">I hope all is well. I am asking about a problem when analyz=
ing a specific structure using the Bio.PDB module. I am trying to calculate=
 the distance between the manganese atom(Mn) and the surrounding ligands wi=
thin a 2.4=C4=82 radius (for oxygen-evolving complex OEX) in the photosyste=
m II (PSII) protein complex, then calculate the average distance for all th=
e resulting distances.</span><br style=3D"font-family:Calibri,sans-serif;fo=
nt-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-size:=
14.6667px">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 alw=
ays less than what=E2=80=99s in PyMol.</span><br style=3D"font-family:Calib=
ri,sans-serif;font-size:14.6667px"><span style=3D"font-family:Calibri,sans-=
serif;font-size: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 variat=
ion is wider than just 0.05!</span><br style=3D"font-family:Calibri,sans-se=
rif;font-size:14.6667px"><br style=3D"font-family:Calibri,sans-serif;font-s=
ize:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-size:14.6=
667px">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 wit=
h 10 different PDB files!=C2=A0</span><br style=3D"font-family:Calibri,sans=
-serif;font-size:14.6667px"><br style=3D"font-family:Calibri,sans-serif;fon=
t-size:14.6667px"><span style=3D"font-family:Calibri,sans-serif;font-size:1=
4.6667px">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-fam=
ily:Calibri,sans-serif;font-size:14.6667px"><br style=3D"font-family:Calibr=
i,sans-serif;font-size:14.6667px"><span style=3D"font-family:Calibri,sans-s=
erif;font-size:14.6667px">Warm regards,</span><br style=3D"font-family:Cali=
bri,sans-serif;font-size:14.6667px"><span style=3D"font-family:Calibri,sans=
-serif;font-size:14.6667px">Salma Yehia</span><br><br><br><br><img width=3D=
"0" height=3D"0" alt=3D"" style=3D"display: flex;" src=3D"https://mailtrack=
.io/trace/mail/e44d634a26d9e0d2de7011c4bdf74dd57bde7a3a.png?u=3D10005938"><=
/div>
_______________________________________________<br>
Biopython mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:Biopython@biopython.=
org" target=3D"_blank">[email protected]</a><br>
<a href=3D"https://mailman.open-bio.org/mailman/listinfo/biopython" rel=3D"=
noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo=
/biopython</a><br>
</blockquote></div>

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