[cctbxbb] cif parser & ccp4 mon_lib incompatibility

[Richard Gildea]

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:
>
> > 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
> > _______________________________________________
> > cctbxbb mailing list
> > cctbxbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/cctbxbb
>
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