[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Nathaniel Echols nechols at lbl.gov
Thu Apr 11 07:49:49 PDT 2013


On Thu, Apr 11, 2013 at 12:17 AM, James Stroud <xtald00d at gmail.com> wrote:
> I downloaded this library, but its failing. Do you know what I'm doing wrong?
>
>   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


Ah, this I think is genuinely our fault - it is requiring that you
have a file which is not part of the CCP4 monomer library at all, but
rather part of a separate curated library ("geostd") which we
distribute.  This is clearly a bug; I'll bug the relevant parties.  I
think you're doing everything else correctly, though.  For now, there
are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif"  which may or
may not work.

2) Just pull out the entire chem_data tree from a Phenix installation
and dump it in /usr/local/cctbx.  Since we want to make this freely
redistributable anyway, this will be a viable long-term solution (and
since it's actually causing problems that this isn't readily
available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if
and when it's committed to SVN.

-Nat


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