- cctbxbb - phenix-online.org

Reducing coordinates to asymmetric unit
by Graeme.Winter＠Diamond.ac.uk 11 Feb '10

11 Feb '10

Hi Folks, Does anyone have a handy bit of CCTBX Python code which will take a spacegroup and unit cell, and a list of coordinates, and return the list of coordinates reduced to the asymmetric unit? I tried the "dumb" approach of: use unit cell and sites -> fractional sites for site in fractional sites: for smx in sg.smx() for ltr in sg.ltr() apply smx, ltr is in asu? return and it did not always return an answer, so there's clearly somthing I don't understand. Fractional coordinates are all in [0,1). I'm sure someone must have done this! Thanks in advance, Graeme Graeme Winter Software and MX Support 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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Bundled boost and scons
by Justin 04 Nov '09

04 Nov '09

Hi all, Is there a possibility to suppress the usage of bundled scons and boost and use the ones installed on the system? This has two reasons: first, I always like to not use bundled things if they are not heavily modified versions. Second,and that is more important in the moment. The bundled boost which I think is 1.39 has problems with >=python-2.6.3 [1]. So I'd like to use the installed boost-1.40 where the problem is already fixed by boost upstreams. Thanks justin [1] AttributeError: 'Boost.Python.StaticProperty' object attribute '__doc__' is read-only http://bugs.python.org/issue7183

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using cctbx and sgtbx module
by hari jayaram 02 Nov '09

02 Nov '09

Hi I am trying to use a Python plugin SuperSymExample which has cctbx modules sgtbx and uctbx as dependencies. I wanted to build these modules for my system python 2.5.2 on ubuntu hardy heron 8.04 64 bit linux. I downloaded the selfx file for the cctbx alone ( without Python) and then had the build complete fully. I used the setpaths utility and then modifies m,y PYTHONPATH. Now after I add the appropriate directories to my PYTHONPATH , if I import sgtbx and uctbx in a python interactive session I get an error ( see below) My PYTHONPATH has: export PYTHONPATH="$PYTHONPATH:/rawdata12/cctbx_standalone/cctbx_sources:/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx" The error I get when I say from cctbx import sgtbx , uctbx: ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject What can I do to avoid the error and use the Plugin correctly. Thanks Hari Detailed error message: hari@charlie:/rawdata12/cctbx_auto/cctbx_build/lib$ python Python 2.5.2 (r252:60911, Jul 22 2009, 15:33:10) [GCC 4.2.4 (Ubuntu 4.2.4-1ubuntu3)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from cctbx import sgtbx,uctbx Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/sgtbx/__init__.py", line 2, in <module> from cctbx import uctbx File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/uctbx/__init__.py", line 1, in <module> from cctbx.array_family import flex File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/array_family/flex.py", line 1, in <module> import scitbx.array_family.flex File "/rawdata12/cctbx_standalone/cctbx_sources/scitbx/array_family/flex.py", line 1, in <module> import boost.optional File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in <module> import boost.python File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in <module> ext = import_ext("boost_python_meta_ext") File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject sys.path: /usr/lib/python2.5/site-packages /rawdata12/wx-widgets-read-only/wxPython /home/hari/ccp4-6.0.99e/share/python /rawdata12/cctbx_auto/cctbx_build/lib /home/hari /rawdata12/cctbx_standalone/cctbx_sources /rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx /usr/lib/python25.zip /usr/lib/python2.5 /usr/lib/python2.5/plat-linux2 /usr/lib/python2.5/lib-tk /usr/lib/python2.5/lib-dynload /usr/local/lib/python2.5/site-packages /usr/lib/python2.5/site-packages /usr/lib/python2.5/site-packages/Numeric /usr/lib/python2.5/site-packages/PIL /home/hari/djtrunk /usr/lib/python2.5/site-packages/kodos /usr/lib/python2.5/site-packages/gst-0.10 /var/lib/python-support/python2.5 /usr/lib/python2.5/site-packages/gtk-2.0 /var/lib/python-support/python2.5/gtk-2.0 /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode

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Strange segementation fault
by Armin Moser 28 Jul '09

28 Jul '09

Dear cctbx-developers, I recently started to use the cctbx. Some days before i may have found a bug. Description: When I import from the cctbx and perform a division through zero (with array objects from numpy) something segfaults. I've appended a script that demonstrates this behaviour. Maybe it's just a problem with my specific system (I did not observe this behaviour on windows). I've compiled the cctbx from the unix sources with the build tag 2008_09_13_0905 on a debian testing system: Python 2.5.4, gcc 4.3.3, libboost.python1.37.0 Do you need information on other libraries too? Can anybody reproduce this or has an idea what could be wrong? Maybe someone can give me a hint how I could try to debug this? Thanks Armin -----------------8<--------------------8<------------ import numpy as np a = np.array([[1,2,3],[4,5,6]]) b = np.zeros(a.shape) b[[0,0,1],[1,2,0]] = 1 c = a/b print 'before import x/0 is not a problem' print c import cctbx from cctbx import xray, crystal, miller, sgtbx, uctbx from cctbx_array_family_flex_ext import miller_index import scitbx_array_family_flex_ext from iotbx.shelx import from_ins lo = b!= 0 c = np.ones(a.shape)*np.inf c_div = a[lo]/b[lo] c[lo] = c_div print 'after import workaround' print c print 'after import x/0 ==> segfault' print a/b

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spec file for cctbx rpm (on F10)
by Cameron Mura 28 Jul '09

28 Jul '09

Hi all, In case it's of interest, I've attached a spec file that works for building a cctbx RPM on Fedora 10 (nothing really F10-specific, so may work on other distros/releases too). Please note that it works by playing the dangerous (and extremely ugly) game of moving the RPM build into the system-wide tree, so it builds "in situ" in /usr/local/cctbx instead of in the RPM default locale (/my/rpm/BUILDROOT/usr/local/cctbx). On the same note, the patch which is referenced in the spec file ('cctbx_bundle_StrucBio.patch') is just a small snippet that edits the head of 'cctbx_install_script.csh' to explicitly control the build path (i.e., override $cwd by explicitly setting something like 'set install_root="/usr/local/cctbx/2009_02_15_2320"', or wherever you'd like cctbx to live...). Probably a much cleaner procedure would be to use the libtbx/configure.py approach in a post-processing step; let me know if anyone pkg's an RPM that way. :-) Enjoy, Cam -- ------------------------------------------------------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cmura(a)virginia.edu Web: http://muralab.org Tel: 434.924.7824 Fax: 434.924.3710 ------------------------------------------------------- #------------------------------------------------------------------------------- # Cameron Mura <cmura(a)virginia.edu>; 27jul09; #------------------------------------------------------------------------------- %define _buildroot /usr/local/cctbx/2009_02_15_2320 %define debug_package %{nil} #%define _builddir /usr/local/cctbx/2009_02_15_2320 Name: cctbx Version: 2009_02_15_2320 Release: 1 Summary: Computational Crystallography Toolbox License: Open Source (BSD-like) Group: Applications/Engineering URL: http://cctbx.sourceforge.net Source0: %{name}_bundle_%{version}.tar.gz Source1: ccp4_mon_lib.tar.gz Packager: Cameron Mura <cmura(a)virginia.edu> Patch0: cctbx_bundle_StrucBio.patch #BuildRoot: /var/tmp/%{name}-buildroot BuildRoot: /usr/local/cctbx/2009_02_15_2320 %description The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system. The goal of the PHENIX project is to advance automation of macromolecular structure determination. PHENIX depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications. The cctbx is designed with an open and flexible architecture to promote extendability and easy incorporation into other software environments. The package is organized as a set of ISO C++ classes with Python bindings. This organization combines the computational efficiency of a strongly typed compiled language with the convenience and flexibility of a dynamically typed scripting language in a strikingly uniform and very maintainable way. Note that CCTBX is developed under an open source (BSD-like) license; for addition information, see http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/cctbx/LICENSE_2_0.txt. %prep # Require weird gymnastics to relocate cctbx outside the RPM build tree... #export MYCCTBXHOME="/usr/local/cctbx/2009_02_15_2320" #if [ ! -d $MYCCTBXHOME ]; then # mkdir -p $MYCCTBXHOME #fi %setup -a 0 -D -c /usr/local/cctbx/2009_02_15_2320 -n . cp %{_topdir}/SOURCES/ccp4_mon_lib.tar.gz /usr/local/cctbx/2009_02_15_2320/. #%setup -a 1 -D -T -c /usr/local/cctbx/2009_02_15_2320 -n . %patch0 -p1 %build /usr/local/cctbx/2009_02_15_2320/cctbx_install_script.csh /usr/bin/python 8 . "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.sh" libtbx.unpack_in_sources ccp4_mon_lib.tar.gz %install mkdir -p $RPM_BUILD_ROOT/usr/local/cctbx/2009_02_15_2320 mv /usr/local/cctbx/2009_02_15_2320/* $RPM_BUILD_ROOT/usr/local/cctbx/2009_02_15_2320/. mkdir -p $RPM_BUILD_ROOT/etc/profile.d echo '. "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.sh"' > $RPM_BUILD_ROOT/etc/profile.d/cctbx.sh echo 'source "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.csh"' > $RPM_BUILD_ROOT/etc/profile.d/cctbx.csh #chmod 755 $RPM_BUILD_ROOT/etc/profile.d/cctbx.sh #chmod 755 $RPM_BUILD_ROOT/etc/profile.d/cctbx.csh #[ $RPM_BUILD_ROOT != "/" ] && rm -rf $RPM_BUILD_ROOT #install -m 755 src/rasmol_32BIT $RPM_BUILD_ROOT/usr/local/rasmol #install -m 755 src/rasmol_XFORMS_32BIT $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 doc/rasmol.hlp $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 INSTALL* $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 README* $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 TODO* $RPM_BUILD_ROOT/usr/local/rasmol #cp -R working/cctbx_sources $RPM_BUILD_ROOT/usr/local/cctbx/%{version} #cp -R working/cctbx_build $RPM_BUILD_ROOT/usr/local/cctbx/%{version} %clean [ $RPM_BUILD_ROOT != "/" ] && rm -rf $RPM_BUILD_ROOT %post #ln -fs /usr/local/rasmol/rasmol_32BIT /usr/local/bin/rasmol %preun #%{__rm} -f /usr/local/bin/rasmol %files %defattr(-,root,root) #%doc ChangeLog.txt ChangeLog.html INSTALL* NOTICE README* /usr/local/cctbx/2009_02_15_2320 /etc/profile.d/%{name}.sh /etc/profile.d/%{name}.csh %changelog * Sun Jul 26 2009 Cameron Mura <cmura(a)virginia.edu) 2009_02_15_2320-1 - Initial RPM build on Fedora 10...

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draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?
by Cameron Mura 06 Jul '09

06 Jul '09

Hi all, Apologies for the message to both mailing lists, but perhaps someone on either cctbxbb or pymol-users has had some recent experience with this... The subject line more-or-less says it all: I'm wondering if anyone has recently used Rob Campbell's draw_symops (or draw_symops_cctbx) Python modules with a relatively recent (within past year) version of the cctbx (particularly the Boost C++ parts) ? I succeeded in doing this a few years ago to generate images such as the ones near the top of http://muralab.org/~cmura/PyMOL/Sandbox/, but I can't get it to work on my present system (64-bit Fedora 10; Python 2.5.2 with Python 2.6 coexisting). Below is what happens when I... 1) Initiate a new PyMOL session (using a PyMOL v1.1 that I built in-place from source, so should be compatible with local python, system libs, etc) 2) load PDB files (tried with a few diff't files; verified that they contain proper CRYST specifications) 3) do the usual 'run draw_symops_cctbx.py' 4) call draw_symops() -- either implicitly, or by explicit specification of the u.c. params (i.e., using something like "draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)") ...which crashes the pymol session and yields the following trace: > PyMOL>draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1) > libc backtrace (48 frames, most recent call last): > /usr/bin/python [0x400649] > /lib64/libc.so.6(__libc_start_main+0xe6) [0x344081e576] > /usr/lib64/libpython2.5.so.1.0(Py_Main+0xb11) [0x34584e7ef1] > *<snip> > ... > ... > </snip>* > /usr/lib64/libpython2.5.so.1.0(PyObject_Call+0x13) [0x345843d493] > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so > [0x7ff19691db16] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x9f) > [0x7ff19692a2ef] > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so > [0x7ff196920b08] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::objects::function::call(_object*, > _object*) const+0x125) [0x7ff196920635] > > /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so(boost::python::detail::caller_arity<2u>::impl<cctbx::sgtbx::rt_mx > (*)(cctbx::sgtbx::space_group const&, unsigned long), > boost::python::default_call_policies, > boost::mpl::vector3<cctbx::sgtbx::rt_mx, cctbx::sgtbx::space_group > const&, unsigned long> >::operator()(_object*, _object*)+0x12a) > [0x7ff18f820a3a] > /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so > [0x7ff18f8034cc] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::throw_error_already_set()+0xe) > [0x7ff196929dde] > /usr/lib64/libstdc++.so.6(__cxa_allocate_exception+0x2f) [0x3444cc2cdf] > /lib64/libc.so.6 [0x3440832f90] > Segmentation fault (libc call stack 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. > PyMOL: abrupt program termination. I tried the recommendation of setting the BOOST_ADAPTBX* env vars, but this doesn't remedy the problem. Also, I tried accomplishing this with many combinations of workflows: 1) old cctbx (e.g., 2005_04_29_1615), latest stable release of cctbx (2009_02_15_2320), bleeding-edge cctbx (2009_07_04_0143) 2) pre-built cctbx binaries versus building myself from src (for each of the above), insuring, again, optimal match between local system libs... 3) cctbx alone, cctbx in the context of Phenix, cctbx +/- its own bundled Python (2.5 and 2.6) Also, I tried this with different combinations of Rob's scripts -- e.g., the 'symop_axes.dat'-dependent "draw_symops.py", versus the 'all_axes_new.py'-dependent "draw_symops_cctbx.py". Interestingly, I found that get_all_axes() from 'all_axes_new.py' works fine for different PDB files. Investigating the above draw_symops stacktrace led me to this post from Ralf Grosse-Kunstleve to python-dev: http://mail.python.org/pipermail/python-dev/2008-September/082639.html It looks like exactly the same problem that's causing the pymol/draw_symops scripts to choke. Also, I can verify that issuing commands such as in Ralf's post (boost_adaptbx.segmentation_fault, boost_adaptbx.divide_by_zero) result in the same segfaults and errors as in his post, so... I believe this is the crux of it. Before delving into Boost codebase, cctbx's exception-handling in C++/Python Boost, etc., I'm wondering if anyone else has seen anything like this...? or has advice on how best to proceed? Any tips or suggestions would be most greatly appreciated. Thanks, Cam -- ------------------------------------------------------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cmura(a)virginia.edu Web: http://muralab.org Tel: 434.924.7824 Fax: 434.924.3710 -------------------------------------------------------

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Reindexing matrix -> transform orientation matrix
by Winter, G (Graeme) 05 May '09

05 May '09

Hi Folks, I'm just trying to figure out how to do the following, given a triclinic orientation matrix (real or reciprocal space, differ by .inverse() -> triclinic unit cell) (like iotbx.lattice_symmetry) stuff -> set of unit cell, Bravais lattice options with reindex operations apply reindex operation to orientation matrix -> new basis a, b, c The former I have historically done using iotbx.lattice_symmetry but given the move from python to cctbx.python, it seems wasteful. I looked at the source code but got a little confused. The latter seems to be more problematic - even reconstructing the change of basis from a known reindexing operation I don't seem to be able to get the right answer :o( Has anyone done anything like this with the CCTBX tools? The context is autoindexing with XDS using a full sweep's worth of images, then inspecting the indexes in SPOT.XDS based on the contents of XPARM.XDS. Thanks, Graeme Graeme Winter Software and MX Support 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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cctbx geometry modules?
by Artem Evdokimov 31 Dec '08

31 Dec '08

Hi, Sorry to ask a possibly obvious question - but I am very new to cctbx and an absolute novice of python :-) Apologies in advance. Quesiton 1 - is there a web site or some other form of a source for a complete cctbx documentation, most importantly with simple working examples? I've been using some of the examples published in the newsletters but they're scattered here and there. Maybe there is a cctbx wiki somewhere? Question 2 - is there anything inside cctbx that can compute elements of protein geometry - such as dihedral angles, planes, etc. (given selections of atoms)? Thanks in advance! Happy New Year! Cheers, Artem

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Re: [cctbxbb] structure factor interpolation
by celine Besnard 19 Nov '08

19 Nov '08

Hi Ralf and Jon, Thanks a lot for your help. I will try to follow your advices. Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

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structure factor interpolation
by celine Besnard 07 Nov '08

07 Nov '08

Hi, I am looking for a function that would allow me to interpolate the structure factors values in between the reciprocal lattice points (h,k,l not integer) so that I can get the reciprocal map not of the whole crystal but of "only one" unit-cell. Is there a simple way to do that in the cctbx ? Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

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