- cctbxbb - phenix-online.org

strange silicon
by Marc Gailhanou 18 Oct '05

18 Oct '05

Hello, I have some trouble with cctbx, I try to understand why and I do not succeed. I need your help ! I replaced quartz with silicon in the "beach in the box" example/tutorial. This is the resulting code : from cctbx import xray from cctbx import crystal from cctbx.array_family import flex silicon_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.4307,5.4307,5.4307,90,90,90), space_group_symbol="Fd3m")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(0.,0.,0.), u=0) ])) silicon_structure.show_summary().show_scatterers() for scatterer in silicon_structure.scatterers(): print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site site_symmetry = silicon_structure.site_symmetry(scatterer.site) print " point group type:", site_symmetry.point_group_type() print " special position operator:", site_symmetry.special_op() f_calc = silicon_structure.structure_factors(d_min=1).f_calc() f_calc.show_summary().show_array() and running the script gives the following result result : Number of scatterers: 1 At special positions: 1 Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si Si 16 ( 0.0000 0.0000 0.0000) 1.00 0.0000 Si: 0.0000 0.0000 0.0000 point group type: -3m special position operator: 0,0,0 Miller array info: None Observation type: None Type of data: complex_double, size=9 Type of sigmas: None Number of Miller indices: 9 Anomalous flag: False Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) (0, 2, 2) 0j (0, 4, 0) (120.217658126+0j) (1, 1, 1) (-84.1884955081+0j) (1, 3, 1) (65.4837172721+0j) (1, 3, 3) (57.4543830832+0j) (1, 5, 1) (-51.4875968695+0j) (2, 2, 2) (128.545406989+0j) (2, 4, 2) 0j (3, 3, 3) (-51.4875968695+0j) The 220 structure factor, at least, does not look correct . I do not understand the 16 multiplicity either. Is there something I miss ? Best regards Marc

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Re: [cctbxbb] differing build and install directories?
by Ralf W. Grosse-Kunstleve 29 Sep '05

29 Sep '05

Hi Bill, Sorry that I dropped the ball on this question before. Erik outlines the best way of creating a portable cctbx bundle, but in this case there may be a simpler alternative: - simply cp -r the installation into the final destination - re-run python .../libtbx/configure.py mmtbx in the new build directory location. This will update all full paths. Note though that this simple approach will preserve all intermediate files created by the build procedure (i.e. all the .o files and some auto-generated C++ files). But please try this out first. If it does what you want we can think about ways of getting rid of the unwanted files. > The other issue is that I need to hard-code in the DYLIB path I hope that we don't have to do this, although I'd be willing to modify the central SConscript to optionally support hard-coded paths if there really is no alternative. > instead > of relying on an environment variable, which I am not allowed to set. All cctbx commands on PATH go through "dispatchers". To see how it works, look at any of the auto-generated scripts in the "bin" subdirectory of the build directory. The dispatchers are basically all the same; only the last few lines differ. Each dispatcher updates PYTHONPATH and DYLD_LIBRARY_PATH "just in time" to finally start the target command. I.e. there are no permanent settings in the environment. You just have to add the "bin" directory to PATH if you don't want to type the full path name to each command all the time (which will also work). Is this going to work for you? Cheers, Ralf

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differing build and install directories?
by William Scott 28 Sep '05

28 Sep '05

Dear Ralf: Sorry to keep pestering you. I'm now trying to build debian packages, which means the build directory differs from the install directory. Because of this, a lot of the shell scripts, python scripts, and compiled binaries in cctbx have a path like /sw/src/fink.build/ ccp4-5.99.3-1/ccp4-5.99.3 hard-coded into them, and I'd like the final one to look like /sw/share/xtal/ccp4-5.99.3 (for example). Similarly for Debian linux. Is there a simple way to build in one directory but use the final install-path for configuring? I've tried changing $install_root in the file cctbx_install_script.csh, but that didn't work. Similarly, I noticed the install_paths hard-coded into the dynamic libraries for cctbx are relative, rather than absolute like the others, for examle: % otool -L cctbx_dmtbx_ext.so cctbx_dmtbx_ext.so: /System/Library/Frameworks/Python.framework/Versions/2.3/ Python (compatibility version 2.3.0, current version 2.3.5) lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.0.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) Is there a simple way to change that? All the best, Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA

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Testing.....
by Erik Mckee 27 Sep '05

27 Sep '05

Hello :) Does this work? I'm surprised there aren't any test messages in the archives before now.... However, perhaps I'm just talking to myself here..... *Tests for echo.....

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