- cctbxbb - phenix-online.org

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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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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