[cctbxbb] cif parser & ccp4 mon_lib incompatibility

[James Stroud]

Hi Nat,

On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote:
> 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 downloaded this library, but its failing. Do you know what I'm doing wrong?

James


chernev 50% cctbx.python ./tst_sa.py
Traceback (most recent call last):
  File "./tst_sa.py", line 267, in <module>
    exercise_1()
  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
    strict=strict)
  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
chernev 51% ls $MMTBX_CCP4_MONOMER_LIB/
total 10248
   0 0/     8 COPYING                    0 g/                   0 n/                    0 u/
   0 1/     0 a/                         0 h/                   0 o/                    0 v/
   0 2/     0 b/                         0 i/                   0 p/                    0 w/
   0 3/     0 c/                         0 j/                2436 pdb_alt_names.txt     0 x/
   0 4/     0 d/                         0 k/                   8 pdb_v2to3.py          0 y/
   0 5/     4 dnarna_basepairs.txt       0 l/                   0 q/                    0 z/
   0 6/     4 dnarna_basepairs_2.txt     0 list/                0 r/
   0 7/     0 e/                         0 m/                   0 s/
   0 8/   104 ener_lib.cif            1340 mon_lib_ind.cif      0 t/
   0 9/     0 f/                      6340 mon_lib_ind2.cif     4 template_link.pdb
chernev 52% echo $MMTBX_CCP4_MONOMER_LIB/
/usr/local/refmac-v5.39/monomers/

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