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@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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