Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility

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

On Wed, Apr 10, 2013 at 3:58 PM, James Stroud wrote: Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg

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> 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

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. James

-Nat