<div dir="ltr">Christian<div><br></div><div>I'm guessing that the ligand was added without hydrogens which would lead to ambiguity about the bond orders.</div><div><br></div><div>Either way, it's better to use the chemical components code as input to eLBOW as this gets all the info needed from the internal database to generate the restraints.</div><div><br></div><div>If you still have bad geometry, send me the input model and restraints.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div><img src="https://monitor-mailtracker.com/pixel/85naAKp4ukd2PvdwbW9v?rid=85naAKp4ukd2PvdwbW9v" width="1" height="1" border="0"></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 22, 2021 at 2:06 AM Christian Tüting <<a href="mailto:christian.tueting@biochemtech.uni-halle.de">christian.tueting@biochemtech.uni-halle.de</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">Dear Phenix-Team, dear Mailing-List,<br>
<br>
I have a question regarding bound ligands during refinement. In our<br>
initial structure, we have multiple spheroidenes bound (pdb ligand id<br>
SPO), but experimental data suggest that it should be speroidenones (pdb<br>
ligand id SPN). The difference between these molecules are located in an<br>
additional oxygen at the head group and a different saturation level of<br>
the carbon chain. I mananged to exchange the molecule using Coot, but<br>
during refinement I got following error:<br>
<br>
<br>
Number of atoms with unknown nonbonded energy type symbols: 602<br>
"HETATM18420 C1 SPN B 600 .*.N C "<br>
"HETATM18421 C10 SPN B 600 .*.N C "<br>
"HETATM18422 C11 SPN B 600 .*.N C "<br>
"HETATM18423 C12 SPN B 600 .*.N C "<br>
"HETATM18424 C13 SPN B 600 .*.N C "<br>
"HETATM18425 C14 SPN B 600 .*.N C "<br>
"HETATM18426 C15 SPN B 600 .*.N C "<br>
"HETATM18427 C16 SPN B 600 .*.N C "<br>
"HETATM18428 C17 SPN B 600 .*.N C "<br>
"HETATM18429 C18 SPN B 600 .*.N C "<br>
... (remaining 592 not shown)<br>
<br>
<br>
So, as far as I understand this error, the ligand is not in the<br>
restrained in the ligand library. I followed this tutorial:<br>
<a href="https://phenix-online.org/documentation/tutorials/elbow.html" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/tutorials/elbow.html</a> to generate<br>
the .cif file for refinement. I was just using the pdb file and the<br>
geometry from there, as it was "coot-refined" and thereby I expected the<br>
correct conformation.<br>
<br>
<br>
The refinement than run fine, but the ligand after refinement is in a<br>
complete wrong conformation and parts of the carbon chain is outside the<br>
density. I am not sure, if this is due to low resolution at these<br>
regions (which are indeed very low compared to other ligands or proteins<br>
in the map), or if during restraining something went wrong.<br>
<br>
Is it possible to add this ligand to the phenix ligand library or do you<br>
have any suggestions, how to improve the restraining using the elbow<br>
tool?<br>
<br>
Thanks in advance<br>
<br>
Christian Tüting<br>
<br>
<br>
<br>
<br>
Dr. rer. nat. Christian Tüting<br>
<br>
Kastritis Laboratory for Biomolecular Research<br>
Cryo-Electron Microscopy & Computational Structural Biology <br>
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