Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility

Hi James, In an empty directory run cctbx_svn_getting_started.csh from libtbx/development 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 cctbx_svn_getting_started.csh cd .. mkdir build cd build /where/is/python/base/bin/python ../sources/cctbx_projects/libtbx/configure.py this_module that_module . setpaths.sh make (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, Graeme 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:

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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 wrote:

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On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

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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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