[cctbxbb] rna3p error

[Haiguang Liu]

Dear Pavel and others,

After looking through the files, I found that the error is due to the
missing dna_rna cif files in the geostd folder.

mmtbx/monomer_library/pdb_interpretation.py calls to
mmtbx/monomer_library/server.py then read the structure information from
geostd folder.

In the release I obtained from server using bootstrap.py, the information
about chem_data was not downloaded (maybe it is in a different location?).

After copying a chem_data to modules, the program works fine.

Best,
Haiguang


On Wed, Aug 30, 2017 at 11:35 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Haiguang,
>
> please send us PDB file and we will investigate.
>
> Thanks,
> Pavel
>
>
> On 8/30/17 07:23, Haiguang Liu wrote:
>
> Dear All,
>
> I recently run into an error while processing DNA molecules using
> pdb_interpreter. The error message is as the following:
>
>  File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/
> monomer_library/pdb_interpretation.py", line 5419, in __init__
>     restraints_loading_flags=restraints_loading_flags)
>   File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/
> monomer_library/pdb_interpretation.py", line 3221, in __init__
>     log=log,
>   File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/
> monomer_library/pdb_interpretation.py", line 2507, in __init__
>     m_j=mm,
>   File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/
> monomer_library/pdb_interpretation.py", line 1693, in get_lib_link
>     return mon_lib_srv.link_link_id_dict["rna3p"]
> KeyError: 'rna3p'
>
> After searching through the threads, I found the same error has been
> reported, but no solution posted. Any suggestion is appreciated.
>
> Best,
> haiguang
>
>
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>
>
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