[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Thu Apr 11 23:10:04 PDT 2013

Hi James,

In an empty directory run




in the cctbx sources - this downloads a source bundle, then moves much of it out of the way and checks out cctbx from svn over the top. I find taking the Python binary from the base of a cctbx binary build a helpful start.

In a nutshell

mkdir cctbx_from_svn
cd cctbx_from_svn
mkdir sources
cd sources
cd ..
mkdir build
cd build
/where/is/python/base/bin/python ../sources/cctbx_projects/libtbx/configure.py this_module that_module
. setpaths.sh

(this is from memory: some of the details re: directories may be shonky and it's early…)

It does work well though. Should also be on the wiki if not already… 

Best wishes,


On 12 Apr 2013, at 06:49, James Stroud wrote:

> 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?
> James
> 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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