[phenixbb] phenix-1.15.2-3472 crashes with multiple CIF's

[Nigel Moriarty]

Oleg

I tried to reproduce the problem but it seems to be your exact files. Can
you send them all off list?

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


On Fri, May 3, 2019 at 7:22 AM <oleg at quantumbioinc.com> wrote:

> phenix-1.15.2-3472 crashes at the very end of the refinement when multiple
> CIF's are given at the command line (see below).
>
> Please have a look.
>
> Thanks
>
> Oleg Borbulevych, Ph.D.
> Staff Scientist
> QuantumBio, Inc.
> 2790 W. College Ave.
> State College, PA 16801
> E-mail: oborbulevych at yahoo.com, oleg at quantumbioinc.com
> Linkedin Professional Profile:
> https://www.linkedin.com/in/oleg-borbulevych-b8045422
>
>
>
>
> ============================== Exporting results
> ==============================
>
> Writing refined structure to PDB file:
>
> /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.pdb
> n_use            =  9639
> n_use_u_iso      =  9639
> n_use_u_aniso    =  0
> n_grad_site      =  0
> n_grad_u_iso     =  0
> n_grad_u_aniso   =  0
> n_grad_occupancy =  0
> n_grad_fp        =  0
> n_grad_fdp       =  0
> total number of scatterers =  9639
>
> Writing refined structure to CIF file:
>
> /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.cif
> Traceback (most recent call last):
>   File
> "/home/oleg/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/refine.py",
> line 11, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File
> "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py",
> line 162, in run
>     refine_object.write_model_cif_file(f_cif_model)
>   File
> "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py",
> line 984, in write_model_cif_file
>     additional_blocks=[cif_block])
>   File
> "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py",
> line 964, in model_as_mmcif
>     restraints = self.extract_restraints_as_cif_blocks()
>   File
> "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py",
> line 862, in extract_restraints_as_cif_blocks
>     if '_chem_comp_plane_atom.comp_id' in loop.keys():
> AttributeError: 'NoneType' object has no attribute 'keys'
>
>
>
>
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