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:
or here: http://psbmini.ucsc.edu/~wgscott/coot/?C=M;O=D
Please let me know if any of these are problematic.
Tuesday, August 27, 2013
Sunday, July 28, 2013
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.
Fairly recently, I created a fink package for rdkit, which coot now depends upon (and makes good use of).
See further details here.
Tuesday, January 1, 2013
Tuesday, October 2, 2012
The OS X fink and pre-build Coot packages are now available.
See further details here.
Tuesday, September 18, 2012
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).
Saturday, September 15, 2012
I am trying to get phaser to use all my processors
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
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" \
(d) Issue the following commands within the phaser src directory:
mv bin bin.orig
--repository=source phaser \
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):
Thanks to Kaspar Hollenstein for help, advice and encouragement.