[phenixbb] Real space refinement not recognizing modified bases from ribosome
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>
> 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb