Dear Phenix-Team, dear Mailing-List, I have a question regarding bound ligands during refinement. In our initial structure, we have multiple spheroidenes bound (pdb ligand id SPO), but experimental data suggest that it should be speroidenones (pdb ligand id SPN). The difference between these molecules are located in an additional oxygen at the head group and a different saturation level of the carbon chain. I mananged to exchange the molecule using Coot, but during refinement I got following error: Number of atoms with unknown nonbonded energy type symbols: 602 "HETATM18420 C1 SPN B 600 .*.N C " "HETATM18421 C10 SPN B 600 .*.N C " "HETATM18422 C11 SPN B 600 .*.N C " "HETATM18423 C12 SPN B 600 .*.N C " "HETATM18424 C13 SPN B 600 .*.N C " "HETATM18425 C14 SPN B 600 .*.N C " "HETATM18426 C15 SPN B 600 .*.N C " "HETATM18427 C16 SPN B 600 .*.N C " "HETATM18428 C17 SPN B 600 .*.N C " "HETATM18429 C18 SPN B 600 .*.N C " ... (remaining 592 not shown) So, as far as I understand this error, the ligand is not in the restrained in the ligand library. I followed this tutorial: https://phenix-online.org/documentation/tutorials/elbow.html to generate the .cif file for refinement. I was just using the pdb file and the geometry from there, as it was "coot-refined" and thereby I expected the correct conformation. The refinement than run fine, but the ligand after refinement is in a complete wrong conformation and parts of the carbon chain is outside the density. I am not sure, if this is due to low resolution at these regions (which are indeed very low compared to other ligands or proteins in the map), or if during restraining something went wrong. Is it possible to add this ligand to the phenix ligand library or do you have any suggestions, how to improve the restraining using the elbow tool? Thanks in advance Christian Tüting Dr. rer. nat. Christian Tüting Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
Christian I'm guessing that the ligand was added without hydrogens which would lead to ambiguity about the bond orders. 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. If you still have bad geometry, send me the input model and restraints. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Thu, Jul 22, 2021 at 2:06 AM Christian Tüting < [email protected]> wrote:
Dear Phenix-Team, dear Mailing-List,
I have a question regarding bound ligands during refinement. In our initial structure, we have multiple spheroidenes bound (pdb ligand id SPO), but experimental data suggest that it should be speroidenones (pdb ligand id SPN). The difference between these molecules are located in an additional oxygen at the head group and a different saturation level of the carbon chain. I mananged to exchange the molecule using Coot, but during refinement I got following error:
Number of atoms with unknown nonbonded energy type symbols: 602 "HETATM18420 C1 SPN B 600 .*.N C " "HETATM18421 C10 SPN B 600 .*.N C " "HETATM18422 C11 SPN B 600 .*.N C " "HETATM18423 C12 SPN B 600 .*.N C " "HETATM18424 C13 SPN B 600 .*.N C " "HETATM18425 C14 SPN B 600 .*.N C " "HETATM18426 C15 SPN B 600 .*.N C " "HETATM18427 C16 SPN B 600 .*.N C " "HETATM18428 C17 SPN B 600 .*.N C " "HETATM18429 C18 SPN B 600 .*.N C " ... (remaining 592 not shown)
So, as far as I understand this error, the ligand is not in the restrained in the ligand library. I followed this tutorial: https://phenix-online.org/documentation/tutorials/elbow.html to generate the .cif file for refinement. I was just using the pdb file and the geometry from there, as it was "coot-refined" and thereby I expected the correct conformation.
The refinement than run fine, but the ligand after refinement is in a complete wrong conformation and parts of the carbon chain is outside the density. I am not sure, if this is due to low resolution at these regions (which are indeed very low compared to other ligands or proteins in the map), or if during restraining something went wrong.
Is it possible to add this ligand to the phenix ligand library or do you have any suggestions, how to improve the restraining using the elbow tool?
Thanks in advance
Christian Tüting
Dr. rer. nat. Christian Tüting
Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
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participants (2)
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Christian Tüting -
Nigel Moriarty