[cctbxbb] cif parser & ccp4 mon_lib incompatibility

James Stroud xtald00d at gmail.com
Thu Apr 11 22:49:27 PDT 2013

Hi Nat,

I'm not sure of the correct way to update with SVN. I compared cctbx_sources and the SVN trunk (which had a .gitignore, suggesting its a git repository). The cctbx_sources from the bundle had some extra directories. Should I do an "svn co" of the trunk and then add the extra directories from the cctbx_sources and then re-build in place?


On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:

> Okay, this problem should be fixed in the latest SVN revision - James,
> could you please update and let us know if you're still seeing
> problems?
> -Nat
> On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
>> 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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