[cctbxbb] cif parser & ccp4 mon_lib incompatibility

James Stroud xtald00d at gmail.com
Wed Apr 10 23:11:54 PDT 2013

On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote:

> On Wed, Apr 10, 2013 at 3:58 PM, James Stroud <xtald00d at gmail.com> wrote:
> Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-
> Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported.  Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice).

I actually iterated through updates until I there were no more. I think I over-shot the sweet spot, though:

chernev 13% setenv MMTBX_CCP4_MONOMER_LIB /usr/local/ccp4-6.3.0/lib/data/monomers/
chernev 14% cctbx.python ./tst_sa.py
Traceback (most recent call last):
  File "./tst_sa.py", line 267, in <module>
  File "./tst_sa.py", line 122, in exercise_1
    pi = get_pdb_inputs(pdb_str=pdb_str_1)
  File "./tst_sa.py", line 108, in get_pdb_inputs
    rama_potential=None, log = None)
  File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object
    mon_lib_srv = mmtbx.monomer_library.server.server()
  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__
    geostd_list_cif_obj = geostd_list_cif()
  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif
  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__
    + ", ".join(mon_lib_env_vars))
mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

> Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:
> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/  [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]
> and this looks like it is formatted correctly.

I'll give this one a try.


> -Nat 
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