- cctbxbb - phenix-online.org

postdoc position in LBNL
by Peter Zwart 21 Oct '08

21 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 -----------------------------------------------------------------

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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

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Re: [cctbxbb] input_atom_labels_list() not available in Python?
by Ralf W. Grosse-Kunstleve 27 Aug '08

27 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.

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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 > >

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interpreting auto generated python interface documentation
by hari jayaram 26 Aug '08

26 Aug '08

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

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Re: [cctbxbb] getting resolution for any "h" "k" "l" and cctbx
by Ralf W. Grosse-Kunstleve 05 Aug '08

05 Aug '08

Hi Hari, > 1) I was wondering if someone can point me to routines available from > cctbx modules that can give me the "resolution" for a given index "h" > "k" "l". in any space group To get the resolution for a given hkl, you just need the unit cell: from cctbx import uctbx uc = uctbx.unit_cell((11,12,13,93,98,103)) hkl = (2,3,4) print uc.d(miller_index=hkl) print uc.stol(miller_index=hkl) wavelength = 1.3 print uc.two_theta(miller_index=hkl, wavelength=wavelength) Save as "resolution_hkl.py" and run with: cctbx.python resolution_hkl.py The .d(), .stol(), .two_theta() methods are documented here: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1uni… > 2) In addition , if someone can point me in the direction of a well > illustrated depiction of the derivation of the reciprocal lattice > for the triclinic case , that will be very much appreciated bonus . I'm not sure which textbook to recommend. I liked the old Buerger books a lot, but I don't remember how he introduces the reciprocal lattice. Ralf

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getting resolution for any "h" "k" "l" and cctbx
by hari jayaram 05 Aug '08

05 Aug '08

Hi , I have been programming in python for a little bit, I am new to cctbx . My crystallography knowledge is as good as solving a few structures gives you. I have a few questions. 1) I was wondering if someone can point me to routines available from cctbx modules that can give me the "resolution" for a given index "h" "k" "l". in any space group 2) In addition , if someone can point me in the direction of a well illustrated depiction of the derivation of the reciprocal lattice for the triclinic case , that will be very much appreciated bonus . Thank you in advance Hari

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Re: [cctbxbb] (no subject)
by Ralf W. Grosse-Kunstleve 26 May '08

26 May '08

Hi Xie, > Are cctbx and phenix compatible with a 64 bit operating system? Yes. > I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Please try the source bundle: cctbx_python_252_bundle.selfx http://cci.lbl.gov/cctbx_build/ Let me know if there are any problems. Ralf

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(no subject)
by Xie Jiabao 26 May '08

26 May '08

Hi, Are cctbx and phenix compatible with a 64 bit operating system? I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Thanks, Xie

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Re: [cctbxbb] problem in "space_group_type"
by Ralf W. Grosse-Kunstleve 16 Apr '08

16 Apr '08

Hi Koen, > The error only occurs when running in Debug mode. In Release mode, > everything works fine, suggesting a memory initialization problem. This is a known feature of Windows: libraries compiled in release and debug mode are not binary compatible. Under Linux I check with valgrind all the time, therefore it is almost certain that the Windows debug/release mix is the only problem. > I'm unable to debug the problem myself or get more details, as I can't > get the library to compile with debugging information in it (Is there an > easy way to do this with the Scons build system? I haven't used Scons > before.) The *one* script to change is libtbx/SConscript Currently, in the if (sys.platform == "win32"): ... if (env_etc.compiler == "win32_cl"): branch you'll find: if (libtbx.env.build_options.debug_symbols): raise RuntimeError("Debug build not supported.") This is the place to start. On Unix platforms it simply works like this: if (libtbx.env.build_options.debug_symbols): opts.insert(0, "-g") I forgot the details of why it is more complicated under Windows. I vaguely recall that there were issues linking with the correct runtime libraries, in particular linking with the correct Python runtime. Idea: replace the RuntimeError above with opts.insert(0, "???") and initialize a new build directory with libtbx\configure.py --build-boost-python-extensions=False --build=debug Since you are not building Python extensions, the Python runtime library problem goes away. Ralf

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