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 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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