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

Pavel Afonine pafonine at lbl.gov
Wed Jun 16 00:28:13 PDT 2021

Hi Firdous,

I've been watching this conversation and I think it reached the point so 
I'm now curious.. Would you mind sharing the model file with us so that 
we evaluate the situation and suggest a way forward? If you choose to 
share files, please send it to me and Nigel, not the whole phenixbb list!


On 6/15/21 22:51, Firdous Tarique wrote:
> 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.
> Best
> Firdous
> On Wed, Jun 16, 2021 at 1:19 AM Nigel Moriarty <nwmoriarty at lbl.gov 
> <mailto: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
>     <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 <http://CCI.LBL.gov>
>     ORCID : orcid.org/0000-0001-8857-9464
>     <https://orcid.org/0000-0001-8857-9464>
>     On Tue, Jun 15, 2021 at 11:14 AM Firdous Tarique
>     <kahkashantarique at gmail.com <mailto: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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