[cctbxbb] cif parser & ccp4 mon_lib incompatibility

Hi James, svn checkout svn://svn.code.sf.net/p/cctbx/code/trunk cctbx_project Should do what you need, and then just use that copy of the sources to replace the cctbx_sources from the bundle. I would copy the extra directories that aren't in the svn trunk so they are alongside the cctbx_project directory (but not inside, just to keep them separate). The usual directory structure amongst the phenix developers is something like: build/ sources/ sources/cctbx_project/ sources/boost/ sources/scons/ Etc. Then cd build/ python ../sources/cctbx_project/libtbx/configure.py mmtbx (or whatever modules you wish to build) source setpaths.sh libtbx.scons -j 2 (number of processors) Luc added the .gitignore because a few of us are using git-svn as our interface to subversion. Hope that helps, Richard On Thursday, April 11, 2013, 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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