<div dir="ltr"><div>Hello Salma,</div><div><br></div><div>Have you computed that example between MN1 and the O1</div><div>ligand "by hand" from the PBD file to get a tie breaker?<br></div><div><br></div><div>Brainstorming about other possible sources of discrepancy:<br></div><div><br></div><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 sometimes an atom is at/on the boundary?<br></div><div><br></div><div>Are you looking at NMR structures with multiple models? if</div><div>so are both scripts looking at the same model or models?<br></div><div></div><br><div>Peter<br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Feb 27, 2024 at 8:50 PM Salma Yahia <<a href="mailto:salmayahia995@gmail.com">salmayahia995@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><span style="font-family:Calibri,sans-serif;font-size:14.6667px">Dear Sir/Madam,</span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="font-family:Calibri,sans-serif;font-size:14.6667px">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.</span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="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 always less than what’s in PyMol.</span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="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 variation is wider than just 0.05!</span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="font-family:Calibri,sans-serif;font-size:14.6667px">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! </span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="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="font-family:Calibri,sans-serif;font-size:14.6667px"><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="font-family:Calibri,sans-serif;font-size:14.6667px">Warm regards,</span><br style="font-family:Calibri,sans-serif;font-size:14.6667px"><span style="font-family:Calibri,sans-serif;font-size:14.6667px">Salma Yehia</span><br><br><br><br><img width="0" height="0" alt="" style="display: flex;" src="https://mailtrack.io/trace/mail/e44d634a26d9e0d2de7011c4bdf74dd57bde7a3a.png?u=10005938"></div>
_______________________________________________<br>
Biopython mailing list - <a href="mailto:Biopython@biopython.org" target="_blank">Biopython@biopython.org</a><br>
<a href="https://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
</blockquote></div>