- cctbxbb - phenix-online.org

Re: [cctbxbb] building sphinx documentation
by Jan Marten Simons 19 Apr '13

19 Apr '13

Am Donnerstag 18 April 2013 19:16:00 schrieben Sie: > Hi Jan, Hi Richard, > I have attempted to build the sphinx documentation using > dox.sphinx/build_docs.sh, and this appears to have run successfully and > produced some html which shows the table of contents etc. However, I can't > seem to find the documentation for any of the significant modules, e.g. > cctbx/xray/structure.py. When I navigate to the link for the structure > module within the xray package > (dox.sphinx/_build/html/cctbx/cctbx.xray.html#structure-module), I see > nothing other than a list of all the modules within the xray package. Am I > missing something here? Have you followed the instructions given in the comments at the top of dox.sphinx/build_docs.sh? Which version of Sphinx do you use? I'm using 1.1.3 regularly and get useful documentation (I've attached the "makescript" I use to build cctbx and the sphinx documentation. If you are interested in it I can also put the output of the sphinx run on my system with current svn on webserver over here.). Has your sphinx build completed successfully or did it abort (e.g. due to out of memory* or due to other problems)? Could you also check if build/dox.sphinx/cctbx/cctbx.xray.rst has all modules listed? > As a novice to using sphinx, I don't like to add significant documentation > in sphinx style without being able to check via generating the > documentation that what I have written is correct sphinx-speak. I can totally understand this ;). Cheers and hopefully we can get this working for you as well, Jan *) For me running sphinx with all those modules selected needs about 3.3 GiB of virtual memory (RAM) and takes a few minutes to actually finish. p.s.: Sorry didn't hit "reply all".

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Finding neighbouring atoms using pair_asu_table
by Lukas Reck 19 Apr '13

19 Apr '13

Dear all, please forgive me if the following is trivial or if I've overlooked something simple, I'm new to cctbx. I'm trying to use the cctbx python libraries to read in a large number of crystal structures and extract some geometric information on the coordination environment of certain atom types in them. I've been following the instructions from the 8/2004 CompComm Newsletter No. 4 at <http://www.iucr.org/__data/assets/pdf_file/0003/6384/iucrcompcomm_aug2004.p…>, pages 22-28 (is that still up to date?) but I cannot seem to get at the correct symmetry elements for each neighbouring atom in the coordination environment of some atom of interest. As far as I understand, the following should be correct: assert(isinstance(structure, cctbx.xray.structure)) # yes, it is a structure asu_mappings = structure.asu_mappings(buffer_thickness = 3) # create the ASU mappings pair_asu_table = cctbx.crystal.pair_asu_table(asu_mappings = asu_mappings) pair_asu_table.add_all_pairs(distance_cutoff = 3) # create the pair ASU table raw_mappings = asu_mappings.mappings() raw_pair_table = pair_asu_table.table() # access to the raw structures for scatterer_index, scatterer in enumerate(structure.scatterers()): # iterate over all atoms in the structure label = scatterer.element_symbol() if label == atom_of_interest: # we are only interested in one atom type for j_seq, j_syms in raw_pair_table[scatterer_index].items(): # j_seq is the neighbouring scatterer's index, j_sym is a list of lists of symmetry indices for sym_group in j_syms: for j_sym in sym_group: # j_sym is an index into raw_mappings[j_seq] print "j_seq:", j_seq, "j_sym:", j_sym print "i_sym_op:", raw_mappings[j_seq][j_sym].i_sym_op() symmetry = asu_mappings.get_rt_mx(j_seq, j_sym) print "%s at %s" % (scatterer.element_symbol(), scatterer.site) print "Neighbour: %s at %s" % (structure.scatterers()[j_seq].element_symbol(), structure.scatterers()[j_seq].site) print "To be transformed by %s (symmetry #%s)" % (symmetry, j_sym) print "into %s" % (symmetry(structure.scatterers()[j_seq].site),) Here's a sample output for one pair of neighbouring atoms: j_seq: 10 j_sym: 1 i_sym_op: 10 V at (0.30204, 0.52919, 0.5) Neighbour: O at (0.36242, 0.49166, 0.5) To be transformed by y-1/2,-x+1/2,z-1/2 (symmetry #1) into (-0.00834, 0.13758, 0.0) As you can see from the coordinates, the neighbouring atom was correctly identified, but the corresponding symmetry as returned by get_rt_mx transforms it into a symmetry equivalent that is very far away. Clearly I misunderstand the function of one or more of the various indices here, but I am not quite clear on where my error lies... Thanks for any pointers! Best regards Lukas Reck -- School of Chemistry Faculty of Engineering, Mathematics and Science Trinity College Dublin Dublin 2 Tel: (+353) 1 896 3452

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building sphinx documentation
by Richard Gildea 19 Apr '13

19 Apr '13

Hi Jan, I have attempted to build the sphinx documentation using dox.sphinx/build_docs.sh, and this appears to have run successfully and produced some html which shows the table of contents etc. However, I can't seem to find the documentation for any of the significant modules, e.g. cctbx/xray/structure.py. When I navigate to the link for the structure module within the xray package (dox.sphinx/_build/html/cctbx/cctbx.xray.html#structure-module), I see nothing other than a list of all the modules within the xray package. Am I missing something here? As a novice to using sphinx, I don't like to add significant documentation in sphinx style without being able to check via generating the documentation that what I have written is correct sphinx-speak. Cheers, Richard

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First svn commit
by James Stroud 18 Apr '13

18 Apr '13

Hello All, Since this is my first commit, I just want to make sure that I have done these things in the appropriate way. Here's what I did: 1. Added a wiki page: https://sourceforge.net/p/cctbx/wiki/Subversion%20set%20up/ 2. Added the method as_miller_arrays_map() to iotbx_mtz_ext.object, which is declared in iotbx/mtz/__init__.py. 3. Added a test for this functionality in the file iotbx/mtz/tst_miller_map.py Please let me know if the manner in which I did anything could use improvement. James

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Euro SciPy
by Graeme.Winter＠diamond.ac.uk 17 Apr '13

17 Apr '13

Hi Folks, Anyone going to this meeting? https://www.euroscipy.org/ Some of the scientific software team here at Diamond have a habit of going to this meeting and remarked that a contribution on CCTBX may be appropriate... (see below for meeting topics) Best wishes, Graeme Topics * Presentations of scientific tools and libraries using the Python language, including but not limited to: * Vector and array manipulation * Parallel computing * Scientific visualization * Scientific data flow and persistence * Algorithms implemented or exposed in Python * Web applications and portals for science and engineering- * Reports on the use of Python in scientific achievements or ongoing projects. * General-purpose Python tools that can be of special interest to the scientific community. -- 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.replace_sites_... vs. structure.set_sites_...
by Jan Marten Simons 16 Apr '13

16 Apr '13

Hi, while working on a really fast way to calculate the structure factors of a few millions of different modifications of a structure with only the selected scatterers contributing to f_calc I came across this: Why are there two methods for changing the sites_(cart/frac) of the scatterers doing quite different things? set_sites_... seems to simply update the corresponding site information of the scatterer, while replace_sites_... seems to create a copy of the structure. Is this the only difference there is? Also If anybody got a nice idea for my original problem, I'm also very much interested. (I think building a larger structure and working with selections might be faster than creating lots of different structures containing only the desired scatterers, but I might be wrong on this.) Cheers, Jan

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pyyaml - iotbx.pdb incompatibility
by James Stroud 16 Apr '13

16 Apr '13

Hello All, There is a strange incompatibility between pyyaml and iotbx.pdb that depends on the order of import. If yaml is imported first, there is no problem. If iotbx.pdb is imported first, then importing yaml crashes. This is the yaml that comes with enthought python, but I don't think it's using libyaml, which is the C implementation. So the yaml, from what I can tell, is pure python. I'm wondering if anyone else can reproduce this error. James chernev 185% cctbx.python Enthought Python Distribution -- www.enthought.com Version: 7.3-2 (64-bit) Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 11:14:05) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "credits", "demo" or "enthought" for more information. py> import yaml py> from iotbx import pdb py> raise SystemExit() chernev 186% cctbx.python Enthought Python Distribution -- www.enthought.com Version: 7.3-2 (64-bit) Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 11:14:05) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "credits", "demo" or "enthought" for more information. py> from iotbx import pdb py> import yaml show_stack(1): /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/yaml/constructor.py(256) SafeConstructor show_stack(2): /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/yaml/constructor.py(161) <module> show_stack(3): /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/yaml/loader.py(8) <module> show_stack(4): /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/yaml/__init__.py(8) <module> show_stack(5): <stdin>(1) <module> libc backtrace (49 frames, most recent call last): 50 python2.7 0x0000000100000f54 start + 52 49 Python 0x0000000100108576 Py_Main + 3318 48 Python 0x00000001000f2c6e PyRun_AnyFileExFlags + 126 47 Python 0x00000001000f2b2e PyRun_InteractiveLoopFlags + 78 46 Python 0x00000001000f28eb PyRun_InteractiveOneFlags + 379 45 Python 0x00000001000cd2c6 PyEval_EvalCode + 54 44 Python 0x00000001000ccfc5 PyEval_EvalCodeEx + 1733 43 Python 0x00000001000c77fe PyEval_EvalFrameEx + 9502 42 Python 0x00000001000c4267 PyEval_CallObjectWithKeywords + 87 41 Python 0x000000010000d052 PyObject_Call + 98 40 Python 0x00000001000be823 builtin___import__ + 131 39 Python 0x00000001000e5cf8 PyImport_ImportModuleLevel + 344 38 Python 0x00000001000e536a load_next + 234 37 Python 0x00000001000e511a import_submodule + 314 36 Python 0x00000001000e4f59 load_package + 409 35 Python 0x00000001000e4632 load_source_module + 466 34 Python 0x00000001000e3981 PyImport_ExecCodeModuleEx + 209 33 Python 0x00000001000cd2c6 PyEval_EvalCode + 54 32 Python 0x00000001000ccfc5 PyEval_EvalCodeEx + 1733 31 Python 0x00000001000c77fe PyEval_EvalFrameEx + 9502 30 Python 0x00000001000c4267 PyEval_CallObjectWithKeywords + 87 29 Python 0x000000010000d052 PyObject_Call + 98 28 Python 0x00000001000be823 builtin___import__ + 131 27 Python 0x00000001000e5cf8 PyImport_ImportModuleLevel + 344 26 Python 0x00000001000e536a load_next + 234 25 Python 0x00000001000e511a import_submodule + 314 24 Python 0x00000001000e4632 load_source_module + 466 23 Python 0x00000001000e3981 PyImport_ExecCodeModuleEx + 209 22 Python 0x00000001000cd2c6 PyEval_EvalCode + 54 21 Python 0x00000001000ccfc5 PyEval_EvalCodeEx + 1733 20 Python 0x00000001000c77fe PyEval_EvalFrameEx + 9502 19 Python 0x00000001000c4267 PyEval_CallObjectWithKeywords + 87 18 Python 0x000000010000d052 PyObject_Call + 98 17 Python 0x00000001000be823 builtin___import__ + 131 16 Python 0x00000001000e5cf8 PyImport_ImportModuleLevel + 344 15 Python 0x00000001000e536a load_next + 234 14 Python 0x00000001000e511a import_submodule + 314 13 Python 0x00000001000e4632 load_source_module + 466 12 Python 0x00000001000e3981 PyImport_ExecCodeModuleEx + 209 11 Python 0x00000001000cd2c6 PyEval_EvalCode + 54 10 Python 0x00000001000ccfc5 PyEval_EvalCodeEx + 1733 9 Python 0x00000001000cb0e6 PyEval_EvalFrameEx + 24070 8 Python 0x00000001000ccfc5 PyEval_EvalCodeEx + 1733 7 Python 0x00000001000c7ea0 PyEval_EvalFrameEx + 11200 6 Python 0x0000000100010af8 PyNumber_Multiply + 40 5 Python 0x000000010000c569 binary_op1 + 137 4 ??? 0x0000000000000aa9 0x0 + 2729 3 libsystem_c.dylib 0x00007fff84b0ccfa _sigtramp + 26 2 boost_python_meta_ext.so 0x00000001007013c0 initboost_python_meta_ext + 0 Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- James Stroud Affiliate Howard Hughes Medical Institute UCLA-DOE Institute for Genomics and Proteomics

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Flex array slice assignment work-alike
by James Stroud 15 Apr '13

15 Apr '13

Hello All, It seems that flex arrays do not support slice assignment: py> from scitbx.array_family import flex py> ary = flex.float(range(5)) py> list(ary) [0.0, 1.0, 2.0, 3.0, 4.0] py> ary[:3] = flex.float([41, 42, 43]) --------------------------------------------------------------------------- ArgumentError Traceback (most recent call last) /usr/local/cctbx/cctbx_sources/mmtbx/dynamics/<ipython-input-13-5ce3d648bc6f> in <module>() ----> 1 ary[:3] = flex.float([41, 42, 43]) ArgumentError: Python argument types in float.__setitem__(float, slice, float) did not match C++ signature: __setitem__(scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, scitbx::af::small<long, 10ul>, float) __setitem__(scitbx::af::versa<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, long, float) Slice assignment is common in python: py> alist = range(5) py> alist[:3] = [41, 42, 43] py> alist [41, 42, 43, 3, 4] Is there a flex array work-alike for this operation? I've found set_selected(): py> sel_ary = flex.bool([True, True, True, False, False]) py> ary.set_selected(sel_ary, flex.float([41, 42, 43])) <scitbx_array_family_flex_ext.float at 0x101df1158> py> list(ary) [41.0, 42.0, 43.0, 3.0, 4.0] But set_selected() is cumbersome for slice assignment because (1) you have to build a flex selection array somehow and (2) you have to put the new values into a flex array of the appropriate type. Is set_selected() the best way? If so, is there something in the cctbx libraries that makes building "slicing" selection arrays more efficient than say a list comprehension? sel_ary = flex.bool([True if i < 3 else False for i in xrange(5)]) James

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cif parser & ccp4 mon_lib incompatibility
by James Stroud 15 Apr '13

15 Apr '13

Hi All, It's a fresh install of the latest-greatest cctbx and of ccp4. Any ideas? % cctbx.python ./tst_sa.py CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days! Here's the top of the cif file: global _lib_name mon_lib _lib_version 5.36 _lib_update 03/05/12 --------------------------------- # # --- LIST OF MONOMERS --- # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group James

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Re: [cctbxbb] [ccp4bb] CCP4 Update victim of own success
by James Stroud 11 Apr '13

11 Apr '13

On Apr 11, 2013, at 6:17 AM, <eugene.krissinel(a)stfc.ac.uk> <eugene.krissinel(a)stfc.ac.uk> wrote: > Sorry that this was unclear. We assume that updater is used primarily from ccp4i, where nothing changed (and why it should be used from command line at all ?:)). Scriptability. On Apr 11, 2013, at 10:34 AM, Jim Pflugrath wrote: > I think James gets to 'fight' like in the old game of rogue by pressing the h, j, k, l keys on his keyboard (not a detachable one either). While Eugene gets to use a modern game controller or a Wii. > > Ooops, game is already over and James [Holton] has lost. But he wrote the game. James

1 1

bin_centers() and d_star_sq
by James Stroud 09 Apr '13

09 Apr '13

Hello All, I'm genuinely perplexed about what factors should go into choosing an appropriate d_star_sq to calculate bin_centers() in cctbx.miller.binner. This decision may be a nuance because it doesn't seem change the output significantly (except for low resolution bins). But if it doesn't matter significantly, then why have the parameter in the first place? James py> binner = miller.setup_binner(n_bins=10) py> binner.show_summary() unused: - 81.7405 [ 0/0 ] bin 1: 81.7405 - 6.1396 [2341/2341] bin 2: 6.1396 - 4.8734 [2213/2213] bin 3: 4.8734 - 4.2574 [2185/2185] bin 4: 4.2574 - 3.8681 [2168/2168] bin 5: 3.8681 - 3.5909 [2177/2177] bin 6: 3.5909 - 3.3792 [2156/2156] bin 7: 3.3792 - 3.2099 [2137/2137] bin 8: 3.2099 - 3.0702 [2144/2144] bin 9: 3.0702 - 2.9520 [2133/2133] bin 10: 2.9520 - 2.8501 [2135/2135] unused: 2.8501 - [ 0/0 ] py> centers = binner.bin_centers(1) py> list(1 / centers) [11.421375552155686, 5.4336997182888345, 4.544594791289144, 4.053431451445772, 3.7243527058119903, 3.481806175995981, 3.292371389128289, 3.138504394416836, 3.0099330507138475, 2.9001646196929975] py> centers = binner.bin_centers(4) py> list(1 / centers**(1 / 4)) [7.301226942489155, 5.330776416864701, 4.514065417212759, 4.039592121777967, 3.716672320747147, 3.4770032890247498, 3.28912114749567, 3.13617782414047, 3.0081962210988116, 2.8988250671976883]

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match_indices.paired_miller_indices() ungraceful overshoot
by James Stroud 08 Apr '13

08 Apr '13

Hello all, I accidentally gave paired_miller_indices() a value > 1 for i_array, and got a segfault. The problem looks to be in match_indices.cpp, line 94: result.push_back(miller_indices_[i_array][pairs_[i][i_array]]); Maybe there should be a test that raises an exception on the python side, if possible. James

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flex and numpy caveats
by James Stroud 06 Apr '13

06 Apr '13

Hello All, I've noticed some incompatibilities between numpy and cctbx, which is understandable. However, the incompatibilities manifest either as nonsense errors or, worse, not at all. Following are a couple of examples I have found. 1. The first example should really throw an exception, because silent failures like this can be catastrophic: py> from numpy import random py> r = random.randint(2, size=10) py> r array([1, 0, 1, 1, 0, 1, 0, 1, 1, 1]) py> list(flex.bool(r)) [True, False, False, False, False, False, False, False, False, False] This example is clearly due to incorrect assumptions about the internal representations of numpy ndarrays. Much better behavior can be seen when using a sequence of python `int` objects: py> list(flex.bool(range(10))) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/jstroud/Unison/Code/radialx/testdata/<ipython-input-754-dce96b02979e> in <module>() ----> 1 list(flex.bool(range(10))) TypeError: No registered converter was able to produce a C++ rvalue of type bool from this Python object of type int 2. Although not as potentially catastrophic as the first, the second example should (in a perfect world) either work or throw a more meaningful exception: py> flex.int(range(10))[r[0]] --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/jstroud/Unison/Code/radialx/testdata/<ipython-input-753-f14587f0ceeb> in <module>() ----> 1 flex.int(range(10))[r[0]] TypeError: 'numpy.int64' object is not iterable This example is obviously a result of type checking for a python `int`. The usual python approach of duck-type checking would avoid this problem: def __getitem__(self, i): try: i = int(i) except: pass return do_whatever_with_i(i) James

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Wilson Plot
by James Stroud 01 Apr '13

01 Apr '13

Hello All, The docsting for cctbx.miller.array.wilson_plot() does not seem to agree with its function (see below). Am I misinterpreting something? James py> miller.wilson_plot.__doc__ '<data^2>' py> miller.wilson_plot() (0.6109909654097065+4.386371170677923j) py> flex.mean(miller.data()) (0.6109909654097065+4.386371170677923j) py> flex.mean(miller.data() * flex.conj(miller.data())) (366421.87112270086+0j) py> flex.mean(miller.data() * miller.data()) (70775.39818541733-1856.4852414296488j)

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Miller array by index
by James Stroud 28 Mar '13

28 Mar '13

Hello All, I ask this question mostly out of curiosity, but what is the most direct way to access the value for a Miller index? The best I can do is the method below, but it seems rather indirect. James py> miller <cctbx.miller.array at 0x107bfa290> py> idx = (0, 0, 2) py> miller.select_indices([idx]).data()[0] (-26338.974329482127+0j)

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Re: [cctbxbb] [ccp4bb] refinement protein structure
by James Stroud 27 Mar '13

27 Mar '13

On Mar 27, 2013, at 12:32 PM, Anastassis Perrakis wrote: > These said, I am rather easily irritated these days, so I will not comment on the irritable character of the email. ... > we will soon start calling disordered loops > positionally challenged polypeptide segments (*). You might want to embrace the power of positive thinking. Where you see "positionally challenged", an optimist would see "entropically gifted". James

1 0

Rotate & translate a structure
by James Stroud 26 Mar '13

26 Mar '13

Hello all, I have a rotation + translation matrix. Let's say py> mtx array([[ 0.88302225, 0.11697778, 0.45451948, 5. ], [ 0.11697778, 0.88302225, -0.45451948, 10. ], [ -0.45451948, 0.45451948, 0.76604444, 20. ], [ 0. , 0. , 0. , 1. ]]) My usual way of transforming a set of coordinates with a 4x4 matrix is to use numpy: py> xyz_1 array([[ 5., 10., 15., 1.], [ 20., 15., 10., 1.]]) py> numpy.inner(xyz_1, mtx) array([[ 17.40268126, 12.59731919, 33.76326397, 1. ], [ 28.9603065 , 21.03969455, 25.38784698, 1. ]]) What is the equivalent in cctbx? Is there a way to avoid converting coordinates back and fourth between numpy arrays with atoms().extract_xyz() & .set_xyz() (as might be used from a iotbx_pdb_hierarchy_ext.root). Thank you for any help. James

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Left to dry by iotbx_pdb_ext.input.construct_hierarchy()
by James Stroud 25 Mar '13

25 Mar '13

Hello all, This seems like it should qualify as a bug. If I have an instance of iotbx_pdb_ext.input and I create a hierarchy with construct_hierarchy(), then I must retain the reference to that hierarchy or apparently I can never get it back: >>> hierarchy = my_pdb.construct_hierarchy() >>> def some_local_scope_function(a_pdb): local_hierarchy = a_pdb.construct_hierarchy() >>> some_local_scope_function(my_pdb) […] RuntimeError: atom has another parent atom_group already. Wouldn't better behavior just return the previously constructed hierarchy given that multiple hierarchies can't be made? If each atom apparently remembers to which atom_group it belongs (and presumably on up), then shouldn't it make sense that an iotbx_pdb_ext.input be able to remember it's own hierarchy and produce it upon demand? Looking at a iotbx_pdb_hierarchy_ext.root, I don't find a reference to the iotbx_pdb_ext.input from which it was created. So, although passing around a hierarchy might be the obvious work-around, the end-user still needs to do some accounting if said user wants to track which roots belong to which inputs, and vice versa. James

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Build Notes for cctbx on OS X 10.7.5
by James Stroud 22 Mar '13

22 Mar '13

Hello All, I spent some time to build cctbx on an OS X 10.7 box for a non-system interpreter. I ran into some kinks along the way, so I thought I'd share my notes in case anyone wants to do the same. These notes are in reStructuredText, so it was no extra work to turn them into the attached HTML file, which might make reading a little easier. James ==================================== Build Notes for cctbx on OS X 10.7.5 ==================================== These notes describe a successful build of cctbx against a specific python interpreter, namely `Enthought python`_ 7.3-2 for x86_64. Although working, versions of cctbx are available for both the system python or with a dedicated python, these canned solutions are not optimal. First, it's not advisable to modify system utilities. Although cctbx seems well-behaved in this regard, other packages may not be so well behaved. Second, the canned approach requires building many of the numerous packages that come with bundeld python distributions like the Enthought distribution (some such packages exceed even cctbx in their difficulty to build). Third, if every package required its own python, every script would need to fire-up dozens of separate interpreters just to do its job, resulting in significant computational overhead with consummately slower execution times. .. _`Enthought python`: http://www.enthought.com/products/epd.php 1. The default c++ compiler for OS X 10.7 is actually clang (``/usr/bin/c++``). Using clang exposes invalid template code. The first of many errors is:: In file included from /opt/cctbx/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent_ext.cpp:7: /opt/cctbx/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h:496:21: error: call to function 'r_factor' that is neither visible in the template definition nor found by argument-dependent lookup r.push_back(r_factor(f_obs, f_model.const_ref())); These types of errors are documented at the page http://clang.llvm.org/compatibility.html#dep_lookup .. note:: The installation directory is ``/opt/cctbx``. 2. I tried to use the HPC compilers at http://hpc.sourceforge.net/, but they do not recognize the ``-no-cpp-precomp`` flag. The web page https://svn.boost.org/trac/boost/ticket/6697 suggests the problem is with boost. However, according to the comments therein, this should have been fixed in boost 1.50. I am building against boost 1.52. Perplexed about the source of this compiler flag, I tracked it down to the file ``cctbx_sources/libtbx/SConscript``, after spending much of a day learning how scons goes about its business. There are two possible fixes: - Comment the following line in ``cctbx_sources/libtbx/SConscript``:: # env_etc.ccflags_base.extend(["-no-cpp-precomp"]) - Link ``/usr/bin/g++`` to ``c++`` in a way that it will be found first in the path. For example:: % ln -s /usr/bin/g++ ${HOME}/bin/c++ 3. I first fixed the ``-no-cpp-precomp`` error by the former, commenting the offending line in ``cctbx_sources/libtbx/SConscript`` but this failed with the error:: /opt/cctbx/cctbx_sources/scitbx/array_family/memory.h:35:47: error: operator '&&' has no right operand #elif defined(_XOPEN_SOURCE) && _XOPEN_SOURCE >= 600 && defined(_POSIX_ADVISORY_INFO) ^ The page http://forums.fedoraforum.org/archive/index.php/t-52929.html suggests that the naked ``_XOPEN_SOURCE`` wrecks the conditional when ``_XOPEN_SOURCE`` is not defined. One possible way to overcome this problem is to change the offending line into a nested if/then, hoping that the comparison never gets evaluated under circumstances when ``_XOPEN_SOURCE`` is not defined:: #elif defined(_XOPEN_SOURCE) #if _XOPEN_SOURCE >= 600 && defined(_POSIX_ADVISORY_INFO) #define SCITBX_AF_HAS_ALIGNED_MALLOC 1 #define SCITBX_AF_USE_POSIX_FOR_ALIGNED_MALLOC 1 #endif #endif However, this was unnecessary because the second fix to the ``-no-cpp-precomp`` error (linking ``/usr/bin/g++`` to ``c++``) worked and avoided changing the preprocessor source. 4. Left to its own devices, scons could not find my ``fftw3.h``, which I have installed (via fink) to ``/sw/include/fftw3.h``. To fix this problem, I inserted the second of the following two lines into the file ``cctbx_sources/libtbx/SConscript``:: env_etc.ccflags_base.extend(["-no-cpp-precomp"]) env_etc.ccflags_base.extend(["-I/sw/include"]) Although this allowed scons to find the header, it could not find the actual library, requiring the insertion of the second of the following lines into the file ``cctbx_sources/libtbx/SConscript``:: env_etc.shlinkflags_bpl = [ "-L/sw/lib", "-w", # suppress "source/lib does not exist" warning "-bundle", "-undefined", "dynamic_lookup"]

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structure_factors() "d_max" equivalent
by James Stroud 21 Mar '13

21 Mar '13

Hello All, I'm new to cctbx and trying to get the most rudimentary understanding. I would like to select all of the reflections within a particular resolution shell. This line from the tutorial: f_calc = quartz_structure.structure_factors(d_min=2).f_calc_array() gets all structure factors through the highest resolution of d_min=2 Å (excluding 0 0 0). My question: is there an equivalent to a d_max argument for this function (i.e. a low resolution limit)? James

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cctbx and symmetry: source code
by prasun kumar 21 Mar '13

21 Mar '13

Dear all I am developing a software for which I needed to use the unit cell generation module of the cctbx. The software will be working for small molecule as well as macromolecule. It will be a great help, if some body can suggest me the part of the program to be used as I am getting confused while selecting the .cpp and .h files. Thanx alot in advance Prasun Kumar PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success

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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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