Fink: coot and coot-pre alternate packages now available

Dear OS X Coot users:

I've updated coot to use a stand-alone refmac, as well as the CCP4 open-source libraries, so all dependencies on proprietary parts of CCP4 should no longer be present.

If you want a recent pre-release, just install "coot".  If it isn't recent enough, either email me, or just grab a pre-compiled nightly version.



You can also do it yourself, if you are in a hurry, just by editing the file

/sw/fink/dists/stable/main/finkinfo/sci/coot.info, changing line 3 (the Revision number) and the corresponding checksum (line 8).


The stand-alone packages will continue to be based upon automatic nightly builds, available here:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot

or here:  http://psbmini.ucsc.edu/~wgscott/coot/?C=M;O=D


Please let me know if any of these are problematic.

The future of Fink's CCP4 package

Now that CCP4 plans to distribute 64-bit binaries for OS X, and has its own update system, the need for a fink package of CCP4 seems less compelling.  I am thinking of creating some sort of "system-ccp4" fink placeholder, and might augment that with a version of the ccp4_setup.xsh files that the user can optionally install.

Any objections?

Coot 0.7.1 stable is now available

The OS X fink and pre-build Coot packages for Coot 0.7.1 are now available.

Fairly recently, I created a fink package for rdkit, which coot now depends upon (and makes good use of).

See further details here.

Some X-ray data from Jan 1st, 2013

Here is how I started the new year:

A permanent invitation to TSA gate rape.

Coot 0.7 stable is now available

Congratulations to Paul Emsley, both for COOT 0.7 and for the new position at the MRC-LMB.  He has certainly earned it.

The OS X fink and pre-build Coot packages are now available.

See further details here.

More changes to the Fink CCP4 package

The main change is to move /sw/share/xtal/ccp4-6.3.0 to /sw/opt/ccp4-6.3.0.  This change of location is to remove a 10 year old violation of fink packaging policy. Briefly, packages with their own unix-like filesystem hierarchy (bin, lib, include, share, etc), should go into /sw/opt/packagename, whereas /sw/share is for platform-indepenent files (text files and so on).

Phaser MPI on OS X: Fink package phaser-mpi

I am trying to get phaser to use all my processors

I've created a fink package called phaser-mpi that does the following automatically:

1. Phaser uses c++ by default (clang++ on OS X).  If you compile phaser using an untouched ccp4-phaser-N.tgz package distributed by CCP4, this works.  If you compile cctbx first, it will fail to compile with clang++.  So you either need to compile both with g++, which you can do by issuing the

--compiler=gcc

directive.  (No other such directive will work, fwiw.)  This is why I had such troubles building phaser for 10.8.1.

2.  Phaser can be tricked into linking the openmpi library by doing the following:

(a)  Install Fink's gcc47 compiler package.

(b)  Unpack CCP4's cctbx/phaser source code.

(c) cd into the ccp4-6.3.0 directory, and issue the following (one-line) command:


perl -pi.orig -e \
"s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= cc.replace\('gcc', 'sw/bin/g\+\+-4'\)|g" \
lib/cctbx/cctbx_sources/cctbx_project/libtbx/SConscript  


(d) Issue the following commands within the phaser src directory:

export CXXFLAGS="-L/sw/lib"
export CFLAGS="-I/sw/include"
export CPPFLAGS="$CFLAGS"

mv bin bin.orig

/usr/bin/python \
../../lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py \
--repository=source phaser \ 
--build-boost-python-extensions=False \ 
--enable-openmp-if-possible=True \ 
--static-exe \ 
--use-environment-flags \ 
--compiler=gcc  

source setpaths.sh  

libtbx.scons -j 8 .  

(e) Restore the original /usr/bin/g++ and /usr/bin/gcc.

(I have 8 processors.  This speeds up the build, but has nothing to do with the outcome.)

(3) Run it using the following KeyWord (in this case for 8 processors):

   JOBS  8  

Thanks to Kaspar Hollenstein for help, advice and encouragement.