- cctbxbb - phenix-online.org

changes to SourceForge project
by Nathaniel Echols 19 Mar '13

19 Mar '13

As promised, the CCTBX SourceForge site has been migrated to their new backend. I am still not sure exactly what this means, but there are two practical changes: 1) The SVN URL has changed - it used to be http://cctbx.svn.sourceforge.net/svnroot/cctbx. Now we have several options. svn checkout --username=natechols svn+ssh://[email protected]/p/cctbx/code/trunk cctbx_project svn checkout --username=natechols https://svn.code.sf.net/p/cctbx/code/trunk cctbx_project svn checkout svn://svn.code.sf.net/p/cctbx/code/trunk cctbx_project The last one is read-only; for the others, replace "natechols" with your SourceForge ID. The old repository is now read-only, so you will need to do a completely new checkout before you can commit any changes you make. Hopefully this will cause minimal disruption; I will change the nightly builds ASAP. 2) As requested, we now have a wiki (completely empty right now): https://sourceforge.net/p/cctbx/wiki/Home/ Feel free to start populating this - if you would like to contribute and don't have access, sign up for a SourceForge account and email me your user ID. -Nat

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Best way to compare two structures using cctbx?
by Jan Marten Simons 12 Mar '13

12 Mar '13

Hi, I think I've seen some code in cctbx which tries to put the similarity of two crystal structures into a number. Am I right on this? I want to have something similar: I'm interested in comparing the direct space atomic distances of two structures sharing the same unit cell parameters and space group and scatterers but different atomic coordinates for those. Now I'd like to have a mapping where I could compare the bond lengths between all scatterers which should eliminate any movements which might also be due to a shift in the origin of a P 1 cell. Also I'd like to have a value for mean, minimal and maximal displacements. The purpose of this is to check how good a structure approximation matches a reference structure. How would you suggest to take on this task? Or is there even some code related to this? Thanks in advance, Jan

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upcoming SourceForge changes
by Nathaniel Echols 27 Feb '13

27 Feb '13

FYI for anyone using CCTBX SVN checkouts: on or about March 9th or 10th, I plan to upgrade our SourceForge project to their new platform, which they claim to want everyone to do in the first quarter of 2013. (I had hoped to do this a month ago but it would have created problems for other projects.) This should give us access to new features including a project wiki, requested by several of you. I am hoping any disruption to SVN access will be minimal and/or quickly resolved (the timing coincides with our Phenix developer workshop so those of us who are attending will be able to fix problems interactively). I'll send out another email after the switch summarizing any changes. -Nat

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pdb shake - dihedral angles
by Dmytro Guzenko 20 Feb '13

20 Feb '13

Hi everyone, I wonder what would it take to write an equivalent to pdb_shake script from iotbx/examples with randomization of the backbone dihedral angles phi and psi, instead of all coordinates perturbation? I want to be able to randomize models in a more "realistic" way. Are there data structures/procedures that can be useful for this in cctbx, or should I extract the coordinates and take it from there? Thanks! Kind regards, Dmytro.

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Re: [cctbxbb] unexpected behaviour of unit_cell.fractionalize
by Jan Marten Simons 14 Feb '13

14 Feb '13

Am Mittwoch 13 Februar 2013 17:01:37 you wrote: > Hi Jan, > > can this method work for you: sites_mod_positive ? I don't remember what > exactly it does but I think it either what you need or at least very close. Hi Pavel, hm, it goes in the right direction, but is not exactly what I'm looking for, as it is bound to scatterers and not to sites in general. And adding a scatterer for each site I want to convert to the structure first, then converting, and than extracting the converted sites from the scatterers afterwards seems quite inefficient to me. Also I think it would be clearer to add the functionality for this to the "fractionalize" function as people trying to convert from direct space coordinates to fractional coordinates will most likely find this functionality first. Cheers, Jan > On 2/13/13 7:17 AM, Jan Marten Simons wrote: > > Hi, > > > > When I try to convert a list of direct space coordinates into fractional > > coordinates like this: > > > > from cctbx import xray > > from cctbx import crystal > > from cctbx.array_family import flex > > > > structure = xray.structure( > > > > special_position_settings=crystal.special_position_settings( > > > > crystal_symmetry=crystal.symmetry( > > > > unit_cell=(3.14098, 4.08327, 5.33966, 83, 109, 129), > > space_group_symbol="P1"))) > > > > sites = flex.vec3_double( ((0.0, 0.1, 0.2), (1.3, 3.0, 2.3), (5.3, 0.1, > > 7.3)) ) sites_frac = structure.unit_cell().fractionalize(sites) > > print(list(sites_frac)) > > > > Now this returns a list of coordinates where x,y,z may be outside ot the > > interval [0,1[. ... quite unexpected. > > > > It would be very nice to have at least an option like "restrict_to_asu" > > in unit_cell.fractionalize which would enforce (x,y,z) to be inside the > > asymmetric unit and/or "restrict_to_cell" which would enforce (x,y,z) to > > be inside the unit cell. > > > > Could any of you more into the inner workings of the cctbx add this > > functionality, please? > > > > Thanks in advance, > > > > Jan

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unexpected behaviour of unit_cell.fractionalize
by Jan Marten Simons 13 Feb '13

13 Feb '13

Hi, When I try to convert a list of direct space coordinates into fractional coordinates like this: from cctbx import xray from cctbx import crystal from cctbx.array_family import flex structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(3.14098, 4.08327, 5.33966, 83, 109, 129), space_group_symbol="P1"))) sites = flex.vec3_double( ((0.0, 0.1, 0.2), (1.3, 3.0, 2.3), (5.3, 0.1, 7.3)) ) sites_frac = structure.unit_cell().fractionalize(sites) print(list(sites_frac)) Now this returns a list of coordinates where x,y,z may be outside ot the interval [0,1[. ... quite unexpected. It would be very nice to have at least an option like "restrict_to_asu" in unit_cell.fractionalize which would enforce (x,y,z) to be inside the asymmetric unit and/or "restrict_to_cell" which would enforce (x,y,z) to be inside the unit cell. Could any of you more into the inner workings of the cctbx add this functionality, please? Thanks in advance, Jan

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Strange behaviour of resolution filter
by Jan Marten Simons 08 Feb '13

08 Feb '13

Hi, I discovered a rather strange behaviour of the miller.index_generator. Sample code showing the weirdness: -----8<--------------------------- from __future__ import division from cctbx import xray from cctbx import crystal from cctbx.array_family import flex structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(3.14098, 4.08327, 5.33966, 83, 109, 129), space_group_symbol="P 1")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(0.,0.,0.), u=0.0)])) fc1 = structure.structure_factors(d_min=1.0).f_calc().sort() d_max, d_min = fc1.resolution_range() fc2 = structure.structure_factors(d_min=d_min).f_calc().sort() print(fc1.size(), fc2.size()) #fc1.show_array() fc1.show_comprehensive_summary() print("\nd_min: {}\n".format(d_min)) fc2.show_comprehensive_summary() #fc2.show_array() -----8<--------------------------- fc1 has 105 indices, while fc2 only has 104. Also fc2 has a higher d_min than fc1 although I'd expect both to have the same. To me it seems like the index with d==d_min is not included and only indices with d>d_min are calculated. I wonder if this behaviour is the desired one or rather a bug, as I was quite surprised when I discovered this. With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University

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Using cctbx::uctbx::unit_cell in c++ code / boosted to Python
by Graeme.Winter＠diamond.ac.uk 25 Jan '13

25 Jan '13

Hi Folks, Been working on some c++ coding using boost etc (which I have to say is great) however I found one bit of weirdness. If I want to generate a cctbx::uctbx::unit_cell in c++ code then access this from Python I get Traceback (most recent call last): File "tst_x2tbx.py", line 67, in <module> tst_x2tbx(sys.argv[1]) File "tst_x2tbx.py", line 6, in tst_x2tbx import x2tbx File "/Users/graeme/svn/cctbx/sources/x2tbx/__init__.py", line 7, in <module> ext = boost.python.import_ext("x2tbx_ext", optional = False) File "/Users/graeme/svn/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 36, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("x2tbx_ext"): dlopen(/Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so, 2): Symbol not found: cctbx::uctbx::unit_cell::unit_cell(scitbx::af::tiny<double, 6ul> const&) Referenced from: /Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so Expected in: flat namespace in /Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so sys.path: …. unless I have import cctbx.uctbx # explicit import at the top of the Python code - have I done something wrong with the SConscript? I found something similar with import scitbx.array_family.flex # explicit import which libtbx.clean_clutter complains about as I don't reference it (hence the additional comment) Equally I could just leave the additional clutter there but it feels like I should not need it... Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Sphinx documentation
by Graeme.Winter＠diamond.ac.uk 21 Jan '13

21 Jan '13

Hi Folks, I installed sphinx and tried building the documentation but I got an error: File ./xfel/xfel.cxi.gfx.rst already exists, skipping. File ./xfel/xfel.cxi.merging.rst already exists, skipping. File ./xfel/xfel.cxi.rst already exists, skipping. File ./xfel/xfel.metrology.rst already exists, skipping. File ./xfel/xfel.rst already exists, skipping. File ./xfel/modules.rst already exists, skipping. sphinx-build -b coverage -d _build/doctrees -D latex_paper_size=a4 . _build/coverage Making output directory... Running Sphinx v1.2pre loading pickled environment... not yet created building [coverage]: coverage overview updating environment: 206 added, 0 changed, 0 removed reading sources... [ 0%] cctbx/cctbx Exception occurred: File "/Users/graeme/svn/cctbx/phenix/phenix-dev-1241/build/mac-intel-osx-x86_64/base/Python.framework/Versions/Current/lib/python2.7/site-packages/Sphinx-1.2predev_20130121-py2.7.egg/sphinx/ext/autodoc.py", line 595, in filter_members membername in self.options.special_members: TypeError: argument of type 'object' is not iterable The full traceback has been saved in /var/folders/j1/cgsqy8fs1lxdyjggcsb3twsw0000gn/T/sphinx-err-jjM5C8.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-users/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [coverage] Error 1 cp: ./_build/coverage/python.txt: No such file or directory cp: ./_build/coverage/c.txt: No such file or directory sphinx-build -b html -d _build/doctrees -D latex_paper_size=a4 . _build/html Making output directory... Running Sphinx v1.2pre loading pickled environment... not yet created building [html]: targets for 206 source files that are out of date updating environment: 206 added, 0 changed, 0 removed reading sources... [ 0%] cctbx/cctbx Exception occurred: File "/Users/graeme/svn/cctbx/phenix/phenix-dev-1241/build/mac-intel-osx-x86_64/base/Python.framework/Versions/Current/lib/python2.7/site-packages/Sphinx-1.2predev_20130121-py2.7.egg/sphinx/ext/autodoc.py", line 595, in filter_members membername in self.options.special_members: TypeError: argument of type 'object' is not iterable The full traceback has been saved in /var/folders/j1/cgsqy8fs1lxdyjggcsb3twsw0000gn/T/sphinx-err-lONSky.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-users/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [html] Error 1 Did I do something wrong? I just grabbed sphinx from the internet. Should I have got it from someplace else? OS X Lion / svn cctbx. Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Phil (dumb) question
by Graeme.Winter＠diamond.ac.uk 14 Jan '13

14 Jan '13

Hi Folks, I have a toy example where I should be overriding Phil defaults: phil_defaults = ''' resolutionizer { rmerge = 0.0 .type = float completeness = 0.0 .type = float isigma = 1.0 .type = float misigma = 2.0 .type = float bins = 100 .type = int } ''' more = ''' resolutionizer { isigma = 2.0 misigma = 4.0 } ''' from libtbx.phil import parse working_phil = parse(phil_defaults) working_phil.fetch(parse(more)) working_phil.show() but it seems I am not: Graemes-MacBook-Pro:scale graeme$ cctbx.python toy.py resolutionizer { rmerge = 0.0 completeness = 0.0 isigma = 1.0 misigma = 2.0 bins = 100 } Am I doing something dumb? I hope so as I really cannot find my error. Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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