- cctbxbb - phenix-online.org

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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Simple cctbx / boost c++ extension example
by Graeme.Winter＠diamond.ac.uk 11 Jan '13

11 Jan '13

Hi Folks, Just say I wanted to write a new from the ground up module for cctbx which wanted to include some C++ code, and a SConscript etc. so I can run libtbx.configure toytbx (say) And then find from toytbx import cplusplus_functions would work.... Is there an example I could follow? (I have not looked through the newsletters, I suppose I should have... but I could not seen anything obvious in the documents) Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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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Computing E^4 from an mtz file
by Graeme.Winter＠diamond.ac.uk 14 Dec '12

14 Dec '12

Hi Folks, Trying to write some code to return the average E^4 across (some) bins for an mtz file, I got to def main(): import sys from iotbx import reflection_file_reader for argv in sys.argv[1:]: reflection_file = reflection_file_reader.any_reflection_file( file_name = argv) if reflection_file.file_type() is None: continue miller_arrays = reflection_file.as_miller_arrays() for ma in miller_arrays: E4(ma) def E4(ma): f = ma.as_intensity_array() f = f.array(data=f.data()/f.epsilons().data().as_double()) f.set_observation_type_xray_intensity() f.setup_binner(auto_binning = True) sm = f.second_moment(use_binning = True) sm.show() if __name__ == '__main__': main() but I have no idea how to actually extract the information I want from sm as this only has show() which gives Graemes-MacBook-Pro:PlayPen graeme$ cctbx.python E4.py /Users/graeme/projects/sci-397/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled.mtz unused: - 20.8668 [ 0/7 ] bin 1: 20.8668 - 5.8873 [221/235] 2.3863 bin 2: 5.8873 - 4.6904 [216/221] 1.9823 bin 3: 4.6904 - 4.1026 [221/222] 1.9925 <snip> bin 47: 1.6553 - 1.6435 [153/209] 2.2051 bin 48: 1.6435 - 1.6320 [143/198] 2.2021 bin 49: 1.6320 - 1.6208 [141/204] 2.7085 unused: 1.6208 - [ 0/0 ] unused: - 20.8668 [ 0/9 ] bin 1: 20.8668 - 7.1654 [201/225] 2.2405 bin 2: 7.1654 - 5.7261 [202/213] 1.9109 bin 3: 5.7261 - 5.0137 [216/223] 2.0162 bin 4: 5.0137 - 4.5605 [207/212] 2.0043 <snip> bin 87: 1.6456 - 1.6393 [126/192] 2.5521 bin 88: 1.6393 - 1.6330 [122/210] 2.0195 bin 89: 1.6330 - 1.6269 [131/224] 2.6251 bin 90: 1.6269 - 1.6208 [120/212] 3.0912 unused: 1.6208 - [ 0/0 ] Really I would like the value programatically or at least a way of getting back an array of the binned values so I can average them myself (which is obviously trivial) Any suggestions? Thanks, Graeme ps - most of this code is ripped from iotbx.reflection_statistics :o) -- 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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Writing a pdb file from an xray_structure object
by Claudia Millán Nebot 12 Dec '12

12 Dec '12

Hi everyone, i have been using the xray_structure_simple() method to get an xray.structure object from a pdb object and use it to perform some calculations on it, one of them being expand it to P1. After, i tried to write a new pdb out of this xray_structure in P1. For that purpose, i used the following method: cctbx.xray.structure.as_pdb_file(self, remark=None, remarks=[], fractional_coordinates=False, resname=None, connect=None) but using it both with the original xray structure and with the one on P1 I get very bad lookings pdbs, with incorrect formating, like that for the case of the one in P1: ATOM 1 PDB= PDB 1 12.330 -6.948 -40.820 1.00 19.26 N ATOM 2 PDB= PDB 2 49.988 55.370 3.948 1.00 19.26 N ATOM 3 PDB= PDB 3 36.092 30.710 93.483 1.00 19.26 N ATOM 4 PDB= PDB 4 55.370 49.988 175.123 1.00 19.26 N ATOM 5 PDB= PDB 5 30.710 36.092 85.587 1.00 19.26 N so i guessed that something must be wrong with the residues.... and went to check the code. That as_pdb_file method calls to iotbx.pdb.xray_structure.as_pdb_file(), and on that code i realised that as i was calling it whithout any resname, it was retrieving it from some information on the scatterers that could be wrong. Putting the value of resname to ALA, as a trial, produced almost the same output except for the name: ATOM 1 PDB= ALA 1 12.330 -6.948 -40.820 1.00 19.26 N ATOM 2 PDB= ALA 2 49.988 55.370 3.948 1.00 19.26 N ATOM 3 PDB= ALA 3 36.092 30.710 93.483 1.00 19.26 N ATOM 4 PDB= ALA 4 55.370 49.988 175.123 1.00 19.26 N ATOM 5 PDB= ALA 5 30.710 36.092 85.587 1.00 19.26 N Up to this point, i don't get what is wrong. It may be that i'm using a too simple method and without the correct parameters (xray_structure_simple()), as i guess part of the error is that the assignation of the types of atoms and residues is going crazy. There are other ways of performing this step from a pdb to an xray_structure and viceversa? Thanks in advance! Best regards, Claudia Millán (cmncri(a)ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain

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Documentation .... again
by Graeme.Winter＠diamond.ac.uk 12 Dec '12

12 Dec '12

Hi Folks, Been thinking some more about the old chestnut of documentation. The lack thereof is a well understood issue, and to be honest one which is not going to change any time soon as no one has the time to maintain a manual - this is fine and well understood. As a kind of "patch" for this I was wondering if it would be possible to have a forum where someone could ask for e.g. documentation for a currently undocumented function, which could then be added to the subversion in the code itself. For example: cctbx_project/cctbx/xray/structure.py ... def structure_factors(self, anomalous_flag=None, d_min=None, algorithm=None, cos_sin_table=False, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None): what is cos_sin_table for? with things like this there is the attitude that it is safe to ignore, however if we're writing code to guide people's experiments it would be good to be sure of this. Some simple documentation explaining this would be very useful. I'm definitely not suggesting (i) that anyone writes a manual or (ii) that all undocumented functions are suddenly documented, only that there is a mechanism set up that someone could ask about this and that someone who knows the answer could commit the changes to cctbx and then reply with the diffs - perhaps the way that stackoverflow works, or an email, or something really lightweight. Even this mailing list could be used I guess? I would be happy to help with this, though the above example is not one where I know the answer! Thoughts? Best wishes, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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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Structure factor calculation weirdness
by Graeme.Winter＠diamond.ac.uk 10 Dec '12

10 Dec '12

Hi Folks, Some confusion here at diamond - it seems that the amplitude of F(hkl) depends on dmin ---------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex # 14keV wavelength = 12.3984 / 14.0 spgroup = 'Fd-3m' latt = (5.4309, 5.4309, 5.4309, 90, 90, 90) atoms = [('Si', 0.125, 0.125, 0.125)] allscatterers=[] for atom in atoms: allscatterers.append(xray.scatterer( label = atom[0], site = (atom[1], atom[2], atom[3]), u = 0)) structure = xray.structure( special_position_settings = crystal.special_position_settings( crystal_symmetry = crystal.symmetry( unit_cell = latt, space_group_symbol = spgroup)), scatterers = flex.xray_scatterer(allscatterers)).expand_to_p1() for dmin in 5.0, 2.5, 1.7: print dmin f_calculations = structure.structure_factors( d_min = dmin).f_calc().amplitudes().show_array() --------------- Chopped out only 001, 010, 100 from this... 5.0 (0, 0, 1) 0.290277589693 (0, 1, 0) 0.290277589693 (1, 0, 0) 0.290277589693 2.5 (0, 0, 1) 0.0 (0, 1, 0) 0.0 (1, 0, 0) 0.0 <snip> 1.7 (0, 0, 1) 0.278378587828 (0, 1, 0) 0.278378587828 (1, 0, 0) 0.278378587828 <snip> Have we misunderstood something? Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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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UB matrix in cbf files
by Carlo.Vecchini＠diamond.ac.uk 04 Dec '12

04 Dec '12

Hello, I would like to add the orientation matrix information in the cbf file. Following the description in sections 3.2.2.2.3 of IUCr (G), I added the following lines in the cbf header: _diffrn_orient_matrix_type ub_matrix_test _diffrn_orient_matrix_UB_11 0.083424 _diffrn_orient_matrix_UB_12 -0.076007 _diffrn_orient_matrix_UB_13 -0.078787 _diffrn_orient_matrix_UB_21 -0.103374 _diffrn_orient_matrix_UB_22 -0.075939 _diffrn_orient_matrix_UB_23 -0.01146 _diffrn_orient_matrix_UB_31 -0.034434 _diffrn_orient_matrix_UB_32 0.043832 _diffrn_orient_matrix_UB_33 -0.156476 When I try to read back the values with: get_orientation_matrix() I get the following error: UBm = cbf_handle.get_orientation_matrix() File "~/CCTBX/cctbx_plus_build/lib/pycbf.py", line 3915, in get_orientation_matrix return _pycbf.cbf_handle_struct_get_orientation_matrix(self) Exception: CBFlib Error(s): CBF_NOTFOUND If I use set_orientation_matrix() to write the cbf file, I get a similar error. Does anyone have any suggestion on how to solve this? Thanks in advance, Carlo Vecchini -- 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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CBF compositing
by Frank Murphy 03 Dec '12

03 Dec '12

Hello, Does anyone have a CCTBX-based method for compositing multiple CBFs to a single image a la merge2cbf? Thanks in advance, Frank Murphy

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OS X Lion + CCTBX + scipy
by Graeme.Winter＠diamond.ac.uk 01 Dec '12

01 Dec '12

Hi Folks, Has anyone got scipy to build against the cctbx python binary distribution on OS X Lion? I am finding that it keeps on compiling some bits of the library for PPC architecture which does not work... Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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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SVN broken?
by Jan Marten Simons 24 Oct '12

24 Oct '12

Hi, while trying to update to the latest svn revision or when trying a fresh checkout I encounter this error: svn co https://cctbx.svn.sourceforge.net/svnroot/cctbx/trunk cctbx_project svn: Can't find a temporary directory: Internal error According to a quick web search the problem is most likely on the svn server (either no disk space or corrupted .svn dir). Hopefully either sourceforge or any of you can fix this. Cheers, Jan

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Re: [cctbxbb] Question about sigma(I) calculation in merge_equivalents
by Kay Diederichs 21 Oct '12

21 Oct '12

Dear Keitaro, Phil, Luc, after looking into the question of how to merge equivalent reflections (in the context of XDS data processing), I am now convinced that cctbx should _not_ use max(internal sigma, external sigma) by default. Why? - it is not obvious to the "end user" of the data that come out of cctbx that this formula was applied (I am not aware that the above formula is clearly documented) - the data processing programs that I know of do not use this formula, but rather use the "external sigma" . I don't imply that the "external sigma" is better, but it violates the principle of least surprise to deviate from a proven procedure. - if the observations (that are merged in cctbx) come from one of these data processing programs then there is a chance that the error model was already adjusted such that the reduced chi**2 is near 1 (at least this is the case for XDS and SCALA). If the sigmas of the merged data then are adjusted upwards again (by the formula above), I have a strong feeling that this leads to an inconsistency. - using max() seems like an ad-hoc way and it lacks a clear rationale. I would like to see examples of comparison of downstream crystallographic calculations (most importantly, experimental phasing) using different ways of calculating the sigma of the merged data. Until this proves the superiority of the above formula, I believe it should be an option, not a default. thanks, Kay > Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp > Thu Sep 6 09:20:34 PDT 2012 > > Previous message: [cctbxbb] Question about sigma(I) calculation in > merge_equivalents > Next message: [cctbxbb] Question about sigma(I) calculation in > merge_equivalents > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > Dear Luc, > > Thank you for your explanation! I understand better than before. > > Usually, sigmas given by data processing programs are already > corrected based on their error model. > Sigmas are adjusted to match the actual scatter. > I think using internal variance is re-correction of sigmas. > Is it valid way? If internal variance is bigger, it suggests error > model is not perfect? > > I calculated external/internal variances using lysozyme (standard > sample in protein crystallography) data. > Intensities and sigmas are determined by XDS. > > I attached two plots, where "Imean", "wsigma", "sigma" are averaged > intensity, internal sigma, external sigma, respectively. > One plot is histogram of wsigma/sigma by multiplicity. For lower > multiplicity, we can see extreme discrepancies. (Note that each > vertical axis is not on the same scale.) > The other plot is wsigma/sigma vs intensity. Extreme discrepancies can > be seen in lower intensities. > I hope it could be interesting for you. > > > > Crystals use only the external variance by default, the reasoning > being that the internal variance being based on sample statistics is > almost always too unreliable because groups of equivalent reflections > are too small. > > Then, I think it would be nice if we can choose the way in cctbx. > I mean, option to choose "use bigger one" or "always use > external/internal variance" would be nice to have. > > I am looking forward to your comment. > > Best regards, > Keitaro > > 2012/9/6 Luc Bourhis <luc_j_bourhis at mac.com>: > > Dear Keitaro, > > > >> But it is still unclear to me why it takes the greatest of the > >> "internal" variance and "external" variance. > >> Is it based on some tests using real data? or is it theoretically > >> superior to using always external variance? > > > > Those are good questions and to be honest I do not know for sure the > answer to them. As it seems common in applied statistics, the treatment > starts with by-the-book methods relying on a well defined theory but at > the end there is always a completely heuristic twist. Particularly true > in crystallography I would argue. But let me try to give some rationales. > > > > It seems to me that the internal and external variance should not > differ too much. Let's consider the two ways this may not be true. > > > > 1. The quoted intensities of a group of equivalent reflections have a > small spread, leading to a small internal variance, but the quoted > sigma's are comparatively big, resulting in an external variance > significantly bigger than the internal one. This is a possible event but > an unlikely one: the statistical intuition in that case is to say that > the small internal variance is a fluke and to use the external one instead. > > > > 2. An external variance significantly smaller than the internal one, > should ring an alarm bell. Indeed a small external variance means that > the small quoted sigma's strongly suggests the intensities cannot spread > too much from their assumed common true value whereas the comparatively > bigger internal variance blatantly contradicts that. Thus either the > intensities or the sigma's have not been correctly determined. > Crystallographers seem to err on the side of trusting data here, i.e. to > disregard the sigma's, and therefore to choose the internal variance. > > > >> I would like to know how this method affects further > crystallographic process. > > > > I am afraid I do not have experience with your domain, protein > crystallography. I know that the small molecule program Crystals use > only the external variance by default, the reasoning being that the > internal variance being based on sample statistics is almost always too > unreliable because groups of equivalent reflections are too small. Since > Crystals is as well accepted as ShelXL to produce publishable > structures, it answer your question in at least in one corner of > crystallography, unfortunately not yours. > > > > I think it could be a simple and interesting exercise to take a > representative protein dataset of yours, then to print the redundancy, > the internal, and the external variance. Actually I would be surprised > if such a study has not already been done and published. Perhaps some of > the gurus on this forum can shed more lights onto that subject. > > > > Best wishes, > > > > Luc -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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FYI: The Quaternion Characteristic Polynomial method
by Jeffrey Van Voorst 19 Oct '12

19 Oct '12

Greetings, If you already know about the quaternion characteristic polynomial method for a fast closed-form solution of the least squares superposition problem, this note is mostly noise. While in the process of updating links to my project, I noticed the note at the bottom of the cctbx sourceforge page (http://cctbx.sourceforge.net/). I like the historical nature presented, and I used the historical method to numerically solve quartic polynomials in a previous project at Michigan State University that ranks relatively large datasets of protein small-molecule binding sites (with respect to a given query site). The superposition method I used has a closed form and is due to BKP Horn. Later on (after writing my dissertation), I found that using the historical method to numerically solve quartic polynomials is not numerically stable or robust. Fortunately, there is an easy solution, and if you are interested in a fast closed-form solution for the least squares superposition problem you would do well (in my opinion) to visit http://theobald.brandeis.edu/qcp/. Best regards, Jeff Van Voorst

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--enable-boost-threads flag
by Jeffrey Van Voorst 19 Oct '12

19 Oct '12

Greetings, If someone knows the answer off the top of their head, I would be interested in the answer. Otherwise, feel free to ignore this. Does the --enable-boost-threads flag for cctbx_sources/libtbx/configure.py do anything drastic besides include -pthread in the compiling and linking steps? I am trying to understand why I would get a free() error (for the shared_ptr to root_data) under the following situation: *) the iotbx_pdb shared library is configured without the --enable-boost-threads flag (on a linux box) *) sometimes reproducible from a test C++ program that is linked using -pthread even in the case when the program is as simple as loading a pdb file and creating the hierarchy. *) gcc 4.4.5 --Jeff Van Voorst

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Re: [cctbxbb] Patterson map data structure
by Ten Eyck, Lynn 16 Oct '12

16 Oct '12

Any Fourier map without an F000 term will analytically have a mean value of 0. Lynn Connected by DROID on Verizon Wireless -----Original message----- From: Nathaniel Echols <nechols(a)lbl.gov> To: cctbx mailing list <cctbxbb(a)phenix-online.org> Sent: Tue, Oct 16, 2012 17:22:17 GMT+00:00 Subject: Re: [cctbxbb] Patterson map data structure On Tue, Oct 16, 2012 at 6:47 AM, Dmytro Guzenko <Dmytro.Guzenko(a)pharm.kuleuven.be> wrote: > rmap = pmap.real_map_unpadded() > n_real = pmap.n_real() > unit_cell = pmap.unit_cell() > grid2cart = maptbx.grid2cart(n_real,unit_cell.orthogonalization_matrix()) > > n_points_total = n_real[0]*n_real[1]*n_real[2] > cart_coord = flex.double(flex.grid(3,n_points_total)) > p_weight = flex.double(n_points_total) > > for plain_ind,grid_point in enumerate(flex.nested_loop(n_real)): > cart_coord[0,plain_ind],cart_coord[1,plain_ind],cart_coord[2,plain_ind] = grid2cart(grid_point) > p_weight[plain_ind] = rmap[grid_point] There are better arrays for storing the coordinates, e.g.: cart_coord = flex.vec3_double(flex.grid(n_real)) p_weight = flex.double(rmap.size()) for plain_ind,grid_point in enumerate(flex.nested_loop(n_real)): cart_coord[grid_point] = grid2cart(grid_point) p_weight[plain_ind] = rmap[grid_point] > By the way, I noticed that many weights are negative, is this possible in a patterson map or am I doing something wrong? This is normal - I believe it's a Fourier series termination error, but I still don't fully understand the reason. An Fobs map will have the same problem; the mean will always be approximately zero. Technically, if the map were perfect with no missing data, it would be uniformly positive, but that's never actually the case. There are ways to "fix" the map so it's all-positive, such as maximum entropy cleanup, but in practice I think we just ignore the negative values (at least for Fobs/2mFo-DFc maps - not sure how Patterson maps are usually handled). -Nat _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb

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Patterson map data structure
by Dmytro Guzenko 16 Oct '12

16 Oct '12

Hello all, I am playing with the Patterson function as calculated by cctbx and I am confused as to how I can extract and manipulate the data. More specifically, miller.patterson_map(...).real_map() returns a one-dimensional array of values. How do I get the corresponding 3D coordinates? I suspect it has to do with the gridding and some kind of fixed order enumeration, but I haven't found an example (the peak_search().sites() seems to be relevant, but I would like the whole thing). On a related note - is there a way to debug the python code of cctbx and step into the c++ code? Debugging is my favorite way to figure things out, but with cctbx most interesting things are hidden. I am using Eclipse + PyDev now. Thank you! Kind regards, Dmytro.

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iotbx.xds
by Graeme.Winter＠diamond.ac.uk 16 Oct '12

16 Oct '12

Hi Folks, Would anyone have any objection if I added some code to iotbx.xds to read things like experimental geometry etc in a straightforward way from the various files that the program produces? I see something to read reflection files in there already. 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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no more Python 2.4
by Nathaniel Echols 15 Oct '12

15 Oct '12

FYI for those of you who didn't get my original email: the minimum Python version required for CCTBX is now 2.5, so for anyone contributing to CCTBX, you can now use more advanced syntax such as "with" and "try/except/else/finally" (and decorators, which were already supported in 2.4, but we haven't used them so far). Full list of changes in 2.5 here: http://docs.python.org/whatsnew/2.5.html -Nat

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