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

Firdous Tarique kahkashantarique at gmail.com
Tue Jun 15 22:51:18 PDT 2021

Hi Nigel

Thanks for this information. To be more specific. If the ribosome contains
many modified bases then I have to generate restraints for each of these
ligands separately and add them one by one using the Real Space Refinement
Add file menu along with the map and the whole 40S coordinates and run it.
Am I right ? Is there anyway If the protein contains multiple ligands and
you want to generate for all in a single output file as it does in refmac,
in that case a single cif file should work for all. I saw one option here
but it says it is generally not preferred to generate restraints for
multiple ligands from the pdb.

My second question is regarding Elbow which is how to use it in its best
possible way, particularly for determining the final geometry of the
ligand. For example the tool suggests that one can *Use simple optimization*,
or *Optimize using elbow AM1 QM method*, or *Optimize using 3rd party QM
package*, or *Provide final geometry from file.*

What do you think? What to use for a general restraint generation for a
ligand from an already known structure.

I am new to Phenix, would appreciate it if you please share with me a
general workflow for using eLBOW and how to use it during refinement.



On Wed, Jun 16, 2021 at 1:19 AM Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Firdous
> You need to generate restraints for the missing entities. You can use
> eLBOW.
> https://www.youtube.com/watch?v=8qVYTUVKlbQ
> and I can help you.
> 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 : 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> wrote:
>> 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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