- cctbxbb - phenix-online.org

spec file for cctbx rpm (on F10)
by Cameron Mura 27 Jul '09

27 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...

1 1

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 -------------------------------------------------------

2 3

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

2 2

cctbx geometry modules?
by Artem Evdokimov 30 Dec '08

30 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

2 1

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

1 0

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

3 3

postdoc position in LBNL
by Peter Zwart 20 Oct '08

20 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

Re: [cctbxbb] interpreting auto generated python interface documentation
by Ralf W. Grosse-Kunstleve 28 Aug '08

28 Aug '08

> Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html, > the documentation gives me a "cache" class __init__ method that says > > __init__(self, root, wildcard_escape_char=r'\') > > How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments. It is a iotbx.pdb.hierarchy.root instance in this case, mostly referred to as "pdb_hierarchy" or just "hierarchy". Yes, for some things you have to go into the code. The best approach is to insert print statements to see what the objects are, then run the associated tests (e.g. iotbx/pdb/tst_*.py). > In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html > return an error page. Thanks for pointing this out. I'll look into this next week, when I'm back home. > I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Don't hesitate to ask. You may have many questions at first, but then they'll become fewer and far in between. I'll respond more promptly after the conference trip. Ralf

1 0

Re: [cctbxbb] input_atom_labels_list() not available in Python?
by Ralf W. Grosse-Kunstleve 26 Aug '08

26 Aug '08

Hi Hari, > input_atom_labels_list() > This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses > this function > However I dont see that in the python interface with the current version? Is that true or am I using a different build > that does not make this available in python That method is gone, indeed, ever since about April/May this year. Look for "atoms_with_labels": cd cctbx_sources libtbx.find_files -g atoms_with_labels -f Ralf P.S.: Have to run now... will look at your other email later.

1 0

input_atom_labels_list() not available in Python?
by hari jayaram 26 Aug '08

26 Aug '08

Thanks Nathaniel.. I too was using the approach of looking at the phenix scripts to figure things out. But I was hoping that there was a "google hidden" source of documentation for the python interfaces that I was not aware of. For the present moment the c++ documentation is much more useful .After I sent the email out , I did notice the section in the manual which says.. "Most documented C++ interfaces are also available at the Python layer. Unfortunately the documentation tools available are not capable of merging the documentations. Therefore Python users need to also consult the C++ documention." On an unrelated note The Nov 2006 newsletter and the c++ and python documentation lists a function in the class iotbx.pdb.input called input_atom_labels_list() This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses this function However I dont see that in the python interface with the current version? Is that true or am I using a different build that does not make this available in python Just curious Hari On Tue, Aug 26, 2008 at 12:50 PM, Nathaniel Echols < nathaniel.echols(a)gmail.com> wrote: > Having spent the last few months trying to learn the python side of cctbx > for my own work, I recommend looking at some of the actual programs that > call these functions (e.g. the various phenix scripts, or testing scripts) > for clues on how to use them. In particular, > iotbx/pdb/tst_atom_selection.py has examples of selection caches. (I'm not > sure how exactly the "cache" class fits in, since it isn't invoked directly > in that script, but hopefully the test script has some approximation of what > you're trying to do.) I haven't found it necessary to look at the C++ code > - boost.python obscures many details anyway, and it's usually pretty obvious > to me what's going on in the python sources based on the > variable/class/function names. > The various CCP4 newsletter articles may have some useful suggestions, but > I haven't looked at these in much detail yet. > > On Tue, Aug 26, 2008 at 9:18 AM, hari jayaram <harijay(a)gmail.com> wrote: > >> Hi , >> I am a few days into learning to use the cctbx libraries. My interests >> are mostly to be able to write scripts that plot various statistics from mtz >> files and use things like iotbx.pdb to manipulate coordinate files. While I >> have managed to write a few scripts and have read the very descriptive >> examples in the newsletters and the few routines inside of phenix. I have >> a problem with getting much out of the python interface documentation at the >> sourceforge site. >> >> Say , for a particular class say >> http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html >> , >> the documentation gives me a "cache" class __init__ method that says >> >> __init__(self, root, wildcard_escape_char=r'\') >> >> How do I find out what "root" is in this example. Should I be looking at >> the c++ code to find out the "types" of these arguments. >> >> In addition a few of the auto-generated documentation pages such as >> http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html >> return an error page. >> >> I just want to know a good way of understanding the varrious interfaces >> when writing code using cctbx in Python >> Thanks in advance >> hari >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/cctbxbb >> >> > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/cctbxbb > >

1 0