[phenixbb] (no subject)

Dorothee Liebschner dcliebschner at lbl.gov
Fri Jun 28 10:27:24 PDT 2019


The message arises when model content is not recognized. This typically
happens for ligand atoms but can also be due to unusual protein atom names.

Check the atom names listed under the message (you actually don't mention
which atoms are mentioned there: CRT atoms or other). If the culprit is
CRT, try adding the .cif file. If it still doesn't work, let us know.

Alternatively, I can have a look at the file. Send me the model and cif
file off-list (!). Don't send files to the entire bulletin board.

Best wishes,


On Fri, Jun 28, 2019 at 7:45 AM Pu Qian <p.qian at sheffield.ac.uk> wrote:

> Hi All
> I have a problem to do refinement for one of our cryo-em model caused by
> ligand of spirilloxanthin (wwPDB code CRT).
> I'm using phenix cryo-EM real-space refinement for one of my cryo-em
> models which contains a ligand called spirilloxanthin, a very common
> carotenoid molecule found in nature. Its code is CRT which can be found in
> wwPDB ligand dictionary and in COOT. However, when I run real-space
> refinement, I got a error message caused by this ligand "Fatal problem
> interpreting model file: Number of atoms with unknot non bonded type
> symbols: xxx please edit the model file to resolve the problem and /or
> supply a cis file with matching restrain definitions, along with
> apply_cif_modification and apply-cis-link parameter definitions if
> necessary". I checked my pdb file. All atom names and order are exactly
> same as that in wwPDB. I also try to insert it into map using COOT monomer
> find method. It does not work as well. It seems to me that Phenix can not
> recognise this ligand, CRT spirilloxanthin. Does anyone have an idea of how
> to deal with this issue. Or is it OK if I add CRT.cif into upload window of
> Phenix for refinement? Any suggestion is greatly appreciated.
> The version of Phenix I am using is Mac version recently downloaded from
> Phenix website.
> Best regards
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Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
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