- cctbxbb - phenix-online.org

programmatic access to PDB through cctbx?
by Kaushik Hatti 01 Apr '15

01 Apr '15

Hello, Sorry if this is not relevant to this mailing list. I was wondering if there are any modules available under cctbx to query PDB database programmatically. There was an option to SQL-query PDBe (from here : http://www.ebi.ac.uk/pdbe-as/pdbedatabase/ ). But, this service has been retired since Mar 2015. How else could complex query on PDB possible? An example query could be: list of PDBid with SCOPid="1hba" and (Resolution < 2 and R/Rfree < 15/20) or (Resolution < 3 and R/Rfree < 20/25 ) and Completeness < 95% and structureFactorAvailability="Y" Such a query was possible via above mentioned SQL link. However, I am unable to find any other means now. Thanks in advance, Kaushik Hatti, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

2 2

dxtbx test failure
by markus.gerstel＠diamond.ac.uk 25 Mar '15

25 Mar '15

Hello everyone, Our last nightly build on RHEL linux x64 failed because the test dxtbx/tests/tst_dxtbx.py , which normally takes roughly 3 seconds to run on the build machine, got stuck for over 5 minutes. All the other tests (cctbx/scitbx/libtbx/iotbx/rstbx and remaining dxtbx) completed successfully. Tests were run via libtbx.run_tests_parallel with nproc=4. As far as I can tell there is no debug output. The libtbx testing suite does not support timeouts like some timeout decorators on python unittest? As far as I can tell tst_dxtbx.py at the moment runs 5 separate tests, so for future debugging it may make sense to split these up. -Markus -- 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

compilation issues
by Dave Lodowski 16 Mar '15

16 Mar '15

Hi, sorry if this is a repeat, but an email sent to the cctbx(a)cci.lbl.gov bounced back to me. We are attempting to install the DIALS package and CCTBX is required for compilation. During compilation of CCTBX, Xrender fails to find the X windows server. OS is Ubuntu LTS 12.04.5 text from console upon failure: Installing Xrender... log file is /home/dave/cctbx/build/base_tmp/Xrender_install_log getting package xrender-0.8.3.tar.gz... downloading from http://cci.lbl.gov/cctbx_dependencies : local copy is current using ./xrender-0.8.3.tar.gz (cached) installing xrender-0.8.3.tar.gz... Traceback (most recent call last): File "../auto_build/install", line 9, in <module> install_base_packages.installer(args=sys.argv, log=sys.stdout) File "../auto_build/install_base_packages.py", line 161, in __init__ self.build_dependencies(packages=packages) File "../auto_build/install_base_packages.py", line 505, in build_dependencies getattr(self, 'build_%s'%i)() File "../auto_build/install_base_packages.py", line 781, in build_render self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "../auto_build/install_base_packages.py", line 407, in build_compiled_package_simple log=pkg_log) File "../auto_build/install_base_packages.py", line 392, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "../auto_build/install_base_packages.py", line 243, in call return call(args, log=log, verbose=self.verbose, **kwargs) File "../auto_build/installer_utils.py", line 71, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/home/dave/cctbx/build/base"' failed with exit code 1 Log file indicates everything fine till X is required then : checking for X... no configure: error: X is required, but it was either disabled or not found. any suggestions as to how to proceed would be appreciated thanks, --David Lodowski

2 1

test 2
by Nicholas Sauter 05 Mar '15

05 Mar '15

-- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

1 0

Atom selections for distance (embarrassingly simple)
by Morten Grøftehauge 18 Feb '15

18 Feb '15

Hi everyone, I'm trying to do some distance extraction of hetero atoms in pdbs. I've got for model in pdb_obj.hierarchy.models(): for chain in model.chains(): for rg in chain.residue_groups(): for ag in rg.atom_groups(): for atom in ag.atoms(): if atom.hetero == True: print atom.distance(atom) Which prints out 0.0 as expected. But I can't figure out how to, say, measure the distance to an atom in the previous residue (if there is a previous residue). I also noticed something weird in this tutorial: http://cctbx.sourceforge.net/sbgrid2008/tutorial.html They truncate a non-standard amino acid to the beta-carbon but this only works because there's an alternate conformation with a standard amino acid (Cys). So it wouldn't work with a seleno-met for instance (I know there's a convert-to-ala function in mmtbx - I said it was weird, not terrible). Anyway, I hope someone can explain the distances thing for me. I'm sure there are multiple ways of doing it (should I just do a selection of "hetatm" and iterate over them and try to get some distanes?). Cheers, Morten

2 1

Partitioning of Grid/Unit Cell
by Nicholas Pearce 15 Feb '15

15 Feb '15

Hi Everyone, I’m trying to partition a grid/space based on smallest distance to atomic sites - as in a voronoi diagram (http://en.wikipedia.org/wiki/Voronoi_diagram <http://en.wikipedia.org/wiki/Voronoi_diagram>). Is there any code in cctbx that could be used to accomplish this? Thanks, Nick Nicholas Pearce, DPhil Student, Structural Genomics Consortium, University of Oxford

3 2

iotbx xray.reconstructed_amplitude and changed SIGF
by Huw Jenkins 12 Feb '15

12 Feb '15

Hi, This is my first post to this list and I hope I can explain my confusion properly. I have been using iotbx to manipulate data stored in mtz files and found that values in columns that should not have been altered by my code are different in the output mtz file. This seems only to occur when the input mtz file contains DANO, SIGDANO columns. When I run the code below F and DANO in input.mtz and output.mtz are the same but SIGF and SIGDANO are different (shown for 5 reflections listed). Is this expected behaviour? Given that in my understanding that code should just read a mtz file, convert the data to a miller array then write the array back out to a new mtz I would expect the values in the input and output to be identical (within rounding error). Thanks, Huw from __future__ import division import sys from iotbx import mtz from iotbx import reflection_file_reader from iotbx import reflection_file_utils def run(args): mtz_file = reflection_file_reader.any_reflection_file("input.mtz") mtz_as_miller_array = mtz_file.as_miller_arrays() f_obs = mtz_as_miller_array[0] mtz_out = f_obs.as_mtz_dataset(column_root_label="F_iotbx") mtz_out.mtz_object().write("output.mtz") if (__name__ == "__main__"): run(sys.argv[1:]) some reflections from input.mtz are: H K L F_ccp4 SIGF_ccp4 DANO_ccp4 SIGDANO_ccp4 ISYM_ccp4 1 2 2 4.90461 2.31536 0 3.27441 0 1 2 3 186.172 1.86381 119.745 3.84862 0 1 2 4 289.31 3.06709 -5.42197 6.46531 0 1 2 5 378.928 2.7118 87.3381 5.56933 0 1 2 6 540.866 4.38513 46.4155 8.8053 0 The same reflections in output.mtz are: H K L F_iotbx SIGF_iotbx DANOF_iotbx SIGDANOF_iotbx ISYMF_iotbx 1 2 2 4.90461 2.00516 0 4.01032 0 1 2 3 186.172 1.8943 119.745 3.7886 0 1 2 4 289.31 3.15096 -5.42197 6.30192 0 1 2 5 378.928 2.74848 87.3381 5.49695 0 1 2 6 540.866 4.3939 46.4155 8.7878 0

2 2

Jenkins spam imminent (but not now)
by markus.gerstel＠diamond.ac.uk 03 Feb '15

03 Feb '15

Hello everyone, We are currently building a continuous integration setup for cctbx using Jenkins at Diamond. This means Jenkins will run all tests for every source code change. If any test (or the build itself) fails, it will send a notification email to this list. This could result in a number of mails. However they follow a pretty obvious format, so should be easy to filter (and we can fine-tune the spamminess if needed). Mails will start soonishly. -Markus -- 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

1 0

Best place to get ccp4io, boost, etc?
by Luc Bourhis 29 Jan '15

29 Jan '15

Hi, I noticed that the nightly build get their dependencies from http://cci.lbl.gov/repositories/ccp4io.gz and the like. Is this the preferred way to make sure one is in synch with trunk then? Best wishes, Luc

2 1

directory of cctbx tutorials
by David Waterman 14 Jan '15

14 Jan '15

Hi all, I've just spent a little time with Google collecting together tutorials for CCTBX and related open-source projects. I'm sure this is not a complete list, so I thought I'd share in case anyone knows of some other sources to add to it. I'm collecting this because the DIALS project is involved in workshops and teaching. My main interest is in diffraction data processing, but all tutorials that use core modules and types from cctbx are of interest, for potential updating/cannibalisation. General/developer - Tour of the cctbx http://cctbx.sourceforge.net/current/tour.html - Making compiled extensions. cctbx_introduction_3 at https://sourceforge.net/p/dials/code/HEAD/tree/trunk/doc/developer/ Data processing - Various tutorials on free-electron laser data processing (cctbx.xfel) at http://viper.lbl.gov/cctbx.xfel/index.php/Tutorials - CCTBX for diffraction calculations. cctbx_introduction_{1,2} at https://sourceforge.net/p/dials/code/HEAD/tree/trunk/doc/developer/ - Powder diffraction unit cell refinement ( <http://cctbx.sourceforge.net/siena2005/>Siena 2005) http://cctbx.sourceforge.net/siena2005/unit_cell_refinement.html - Data processing with DIALS. 4 tutorials at http://dials.sourceforge.net/doc/index.html Coordinate handling - PDB truncate to Ala (SBGrid 2008) (iotbx.pdb) at http://cctbx.sourceforge.net/sbgrid2008/tutorial.html Phasing - Direct methods (Siena 2005) http://cctbx.sourceforge.net/siena2005/direct_methods_light.html Model refinement - Rigid body refinement (IUCr 2008) at http://cctbx.sourceforge.net/iucr2008/rigid_body_refinement_core.html -- David

2 1