October 2015 - cctbxbb - phenix-online.org

dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

2 2

Failure in phenix.map_box when working with map files....
by Ezra Peisach 11 Dec '15

11 Dec '15

Has anyone observed a failure of phenix.map_box when working with map files? When working with a structure factor file with map coefficients, it works fine. When a map file is used - the following occurs: Traceback (most recent call last): File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 194, in <module> run(args=sys.argv[1:]) File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 158, in run selection = selection) File "/local/scratch/CCTBX/cctbx_sources/mmtbx/utils/__init__.py", line 2938, in __init__ self.map_box = maptbx.copy(map_data, gridding_first, gridding_last) Boost.Python.ArgumentError: Python argument types in cctbx_maptbx_ext.copy(double, list, list) did not match C++ signature: copy(scitbx::af::const_ref<double, cctbx::maptbx::c_grid_padded_p1<3ul> > map_unit_cell, scitbx::af::tiny<int, 3ul> first, scitbx::af::tiny<int, 3ul> last) copy(scitbx::af::const_ref<float, cctbx::maptbx::c_grid_padded_p1<3ul> > map_unit_cell, scitbx::af::tiny<int, 3ul> first, scitbx::af::tiny<int, 3ul> last) copy(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > map, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > result_grid) copy(scitbx::af::const_ref<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > map, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > result_grid) Any suggestions? The map_data is the same format in the call....

4 5

Unused/old modules on the top-level of cctbx
by Oleg Sobolev 18 Oct '15

18 Oct '15

Hi, I went through top-level directories of cctbx and discovered the following: compcomm - two papers from IUCr computational crystallography authored by Ralf with some scripts. These scripts are referenced in these papers. One paper in LaTeX by Luc Bourhis "Small-molecule toolbox". dox - probably was meant as documentation, actually contains some documentation in RST, Ralf's talks from Siena, 2005, some tutorial in LaTeX, the content for the cctbx website. fftw3tbx - probably is not used anywhere ipctbx - most likely is not used anywhere, wrapper for sys/ipc.h - C library for interprocess communication access structure. rpmbuild - not sure whether it is still needed/working, last change to the only file was on 7-29-2009. setup - not clear whether the only .sh script in this directory is still needed/working. I suggest to move compcomm to dox despite the reference in 2009 paper and remove fftw3tbx, ipctbx, rpmbuild, setup if nobody has an idea why they should stay where they are/be moved somewhere. Best regards, Oleg Sobolev.

3 3

cctbx documentation
by Paul Adams 13 Oct '15

13 Oct '15

Dear Colleagues, we are looking at the cctbx documentation. Currently the world is directed to the documentation on the Sourceforge site, which hasn’t been updated for a long time and is looking somewhat old. Last year, Oliver and Ian (and others) worked on Sphinx-based documentation for cctbx (the last published version of which can be found here: http://cci.lbl.gov/cctbx_docs/). The question for the cctbx developer community therefore is whether we should move over to the Sphinx system for cctbx documentation. The benefits are: a more consistent and modern interface, and automated documentation generation from source code header file information. As part of making this move we would need to integrate some of the additional information from the original cctbx site into the Sphinx documentation. We would also move the hosting of the cctbx documentation to the CCI web server in Berkeley (and off the Sourceforge site). Another email related to that topic soon. I’d appreciate any feedback on this topic. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

2 1

cctbx and Github
by Paul Adams 11 Oct '15

11 Oct '15

Dear Colleagues, there has been some discussion in this bulletin board about moving the cctbx repository from Sourceforge to Github. We are seriously considering this option, especially in light of the Sourgeforge outage earlier in the year. One concern is what impact this will have on the cctbx developer community - which goes beyond Phenix and DIALS. We’d appreciate any feedback about this proposed move. Note that this will take some time to orchestrate and will involve contacting any known users of the cctbx package to inform them of the change. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0