[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!
Pavel
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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