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/