[phenixbb] (no subject)

Pu Qian p.qian at sheffield.ac.uk
Fri Jun 28 07:42:37 PDT 2019

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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