[phenixbb] Real space refinement not recognizing modified bases from ribosome

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jun 15 12:48:51 PDT 2021


You need to generate restraints for the missing entities. You can use eLBOW.


and I can help you.



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 Tue, Jun 15, 2021 at 11:14 AM Firdous Tarique <kahkashantarique at gmail.com>

> Hi
> I am trying to do real space refinement of a 40S rigid body docked model
> in a cryoEM map of 4.8 Angstrom resolution. The PDB contains some modified
> nucleic acid bases  due to which the program ends with the following error.
> Fatal problems interpreting model file: Number of atoms with unknown
> nonbonded energy type symbols; 52 Please edit the model file to resolve the
> problems and /or supply a CIF file with matching restraint definitions,
> along with apply_cif_modification and apply_cif_link parameter definitions
> if necessary.
> Seems its refinement library is not able to read the modified bases. Can
> you please advise how to fix this problem. What is the best way to update
> the library ? Any suggestions are highly appreciated.
> Best
> Firdous
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