[phenixbb] Ligand Library

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 22 12:44:39 PDT 2021


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.



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
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 <
christian.tueting at biochemtech.uni-halle.de> 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
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> tel: +49 345 5524985
> web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
> web (HALOmem): https://www.halomem.de/en/
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