- cctbxbb - phenix-online.org

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

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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

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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

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Boost Import Error
by Garrett Thompson 12 Jan '15

12 Jan '15

Hello, I recently looking at the cctbxbb mailing archive and I came across your email response a few months ago : http://phenix-online.org/pipermail/cctbxbb/2014-June/000933.html I was wondering if you could elaborate a bit on how to use the wrappers cctbx.python? I consider myself to be quite a beginner in this area and can't seem to import the same module, import scitbx.array_family.flex *ImportError: No module named boost.optional* When I do I receive the same error about having boost.optional being an import dependency. If you are able to, please be as explicit as possible, I am pretty bad with common conventions and terminology, as I have never studied computer science or any related area formally. Any help would be much appreciated! Sincerely, Garrett Thompson

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e density from atomic model?
by TJ Lane 06 Jan '15

06 Jan '15

Crystallography pros, Field-outsider asking for advice here. Is there a standard way to estimate the electron density on a grid from an atomic model (e.g. PDB coordinates of atoms)? One thing that occurred to me was to simply FT the Cromer-Mann atom-centered Gaussians commonly used to model atomic form factors. Perhaps there is a more standard way, though? And possible code to mooch...? Thanks much! TJ

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building on Mac OSX
by Roger Martin 05 Jan '15

05 Jan '15

Hi, I'm attempting to build on Mac. Via jenkins. The scons finds /usr/bin/c++ but my builds are based on gcc located at /opt/gcc/current/bin. A which c++ returns /opt/gcc/current/bin/c++. I tried to tell it by making a site_init.py according to http://www.scons.org/doc/production/HTML/scons-user.html#idm12919064 --------------- cd build mkdir -p site_scons cat <<EOF >./site_scons/site_init.py env = DefaultEnvironment(tools = ['gcc', 'gnulink'], CC = '/opt/gcc/current/bin/gcc', CXX = '/opt/gcc/currentbin/g++') EOF -------------- Do you have a way to tell it which compiler version to find that is compatible with the source code level? Regards, Roger

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building from cctbx SVN repository
by Roger Martin 11 Dec '14

11 Dec '14

Hi, http://cctbx.sourceforge.net/current/installation.html shows svn export svn://svn.code.sf.net/p/cctbx/code/trunk/libtbx/development/cctbx_svn_getti… ./cctbx_svn_getting_started.csh where cctbx_svn_getting_started.csh starts with a curl: curl http://cci.lbl.gov/cctbx_build/results/current/cctbx_bundle.selfx -o cctbx_bundle.selfx yet currently http://cci.lbl.gov/cctbx_build/results/current/cctbx_bundle.selfx doesn't exist. http://cci.lbl.gov/cctbx_build/results/current/ and has the Nov 13 bundle. Has the build changed or this url http://cci.lbl.gov/cctbx_build/results/current/cctbx_bundle.selfx really missing? Thank you, I'm wanting to be at svn HEAD for development in case I find something to add or patch. Roger

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Correlation coefficient for symmetry-related reflections
by Vanbenschoten, Andrew 08 Dec '14

08 Dec '14

Hi everyone, I'm analyzing a diffraction dataset with very weak intensities and I'm getting extremely high R-linear values. Though this may simply be due to poor data, I'd like to calculate the correlation coefficient between sets of symmetry-related reflections to make sure the low intensity values aren't artificially inflating the observed R-linears. Is there a way to do this in Phenix or cctbx? Thanks! -Andrew

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mean weighted phase error by resolution bin
by Mooers, Blaine H.M. (HSC) 05 Dec '14

05 Dec '14

Thanks to Pavel's suggestion, I was able to calculate the overall mean weighted phase error between to sets of phases in miller_arrays 2 and 5. I am stumped on how to retrieve the mean weighted phase error by resolution bin. #! /usr/bin/env cctbx.python import sys import iotbx mtz_filename = sys.argv[1] mtz_file = mtz.object(mtz_filename) miller_arrays = mtz_file.as_miller_arrays() binner=miller_array.setup_binner_d_star_sq_step(d_star_sq_step=0.01) mwpe = miller_arrays[2].mean_weighted_phase_error(miller_arrays[5]) Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/… Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma… X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/… ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Wednesday, December 03, 2014 2:00 PM To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 69, Issue 3 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Re: computing mean phase error between final refined model and experimental phases (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Tue, 02 Dec 2014 12:06:08 -0800 From: Pavel Afonine <pafonine(a)lbl.gov> To: cctbx mailing list <cctbxbb(a)phenix-online.org>, Blaine-Mooers(a)ouhsc.edu Subject: Re: [cctbxbb] computing mean phase error between final refined model and experimental phases Message-ID: <547E1BB0.3030103(a)lbl.gov> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Blaine, key functionality for this is the method of Miller array class called mean_phase_error, see: cctbx/miller/__init__.py . Unit and regression tests are best usage examples most of the time. In this case see: cctbx/regression/tst_miller.py . Let me know if you have any questions. I don't have a good grasp of phase error value as a quality measure. For example, I do not know what number is good, what is poor, etc. I think to some extent what you are trying to do can be converted to Fourier map comparison: just compute two maps, each one using identical amplitudes and two different sets of phases, and then compare maps. To me at least the map CC is a more telling metric. However, map comparison is tricky too (usual map CC may be misleading!) and you need to use proper metrics, as explained in details here: Acta Cryst. (2014). D70, 2593-2606. Metrics for comparison of crystallographic maps A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams Pavel On 12/2/14 9:20 AM, Mooers, Blaine H.M. (HSC) wrote: > Dear CCTBXBB, > > I want to compare the phases from the final refined model and a set of > experimental phases > to calculate the weighted mean phase error. > > How do I this using python? > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Assistant Professor > Department of Biochemistry and Molecular Biology > University of Oklahoma Health Sciences Center > S.L. Young Biomedical Research Center Rm. 466 > > Shipping address: > > > office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 > e-mail: blaine-mooers(a)ouhsc.edu > > Faculty webpage: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_depa… > > Small Angle Scattering webpage: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs… > > X-ray lab webpage: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_depa… > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai…

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computing mean phase error between final refined model and experimental phases
by Mooers, Blaine H.M. (HSC) 02 Dec '14

02 Dec '14

Dear CCTBXBB, I want to compare the phases from the final refined model and a set of experimental phases to calculate the weighted mean phase error. How do I this using python? Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/… Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma… X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…

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structure factors from map
by castro＠biochem.mpg.de 01 Dec '14

01 Dec '14

Hi, Could somebody please help to find the function to transform electron density map into structures factors? I found a function "from_map()" within cctbx/maptbx/structure_factor.h, But it don't know how to transform the map into a "complex_map" format. Thanks a lot in advance, Marcelino

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Problem with executing Pymol with Tk (I build it with cctbx)
by Tam＠em.uni-frankfurt.de 17 Nov '14

17 Nov '14

Dear all, I have a problem to execute Pymol that it is without external GUI and just only the Viewer window. This is the error message I got after executing the pymol. Traceback (most recent call last): File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/pymol/__init__.py", line 401, in launch_gui __import__(self.invocation.options.gui) File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/pmg_tk/__init__.py", line 22, in <module> from PMGApp import * File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 28, in <module> from Tkinter import * File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: No module named _tkinter Thanks for the help. Regards HK

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using the c++ fft_to_real_map_unpadded to make maps
by Roger Martin 14 Nov '14

14 Nov '14

Hi, I posted to the sourceforge help forum: http://sourceforge.net/p/cctbx/discussion/76274/thread/16122dcc/ about using fft_to_real_map_unpadded. Have had great success with it making maps for visualizing results. What I'm not understanding is the shape and properties of maps for 'P 32 2 1' and other space groups that have translations of 1/3, 1/4 or 1/6 in symmetry operators. Is there something special or extra that needs done for the fourier coefficients, n_real dimensions or the returned versa map? cctbx::sgtbx::space_group spaceGroup(cctbx::sgtbx::space_group_symbols(154)); const scitbx::af::int3 n_real(n, m, l); scitbx::af::versa< double, scitbx::af::c_grid<3>> pDelta=cctbx::maptbx::fft_to_real_map_unpadded(spaceGroup, n_real, miller_indices.const_ref(), structure_factors.const_ref()); Looking inside I see it does tha padding for me. So running out of things to try. Any ideas would be appreciated --Roger

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Electron density hitogram from MTZ file
by castro＠biochem.mpg.de 28 Oct '14

28 Oct '14

Hi everybody, I am new in crystallogrphy and in the use of cctbx. I am interested in building a electron density histogram from a mtz file. Could somebody give a hint on how to accomplish this task using cctbx libraries (I am scripting in python)? Let's say that I already have the columns of interest as "miller arrays". Then (I think), a grid (on the real space) needs to be created based on unit cell parameters, to finally make the fft. I think that most of my doubts are about the grid. How small the grid should be with respect to the low-resolution limit? Does the space group information needed or it is enough with the the cell parameters? Is there all ready a routine doing this? Thanks a lot for your help. Marcelino

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which cctbx version is recommended now?
by Marcin Wojdyr 15 Oct '14

15 Oct '14

Hi, we need to pick a version of cctbx for CCP4 for use in phaser and DIALS. The latest logs at cci.lbl.gov/cctbx_build/show_error_summary.cgi?build_tag=2014_10_05_2205 show in all builds: [Errno 2] No such file or directory Traceback (most recent call last): ImportError: __import__("boost_python_meta_ext"): No module named boost_python_meta_ext Is it better to pick older version? Marcin

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Miller arrays from lists of indices
by Oliver Zeldin 07 Oct '14

07 Oct '14

Dear cctbx devs, Does anyone know how to make a miller set from a list of (h, k, l) indices? e.g. [(1,2,3), (34, 1, 45), .... ] Cheers, Oliver -- Dr. Oliver B. Zeldin Brunger Group Stanford University

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new cctbx-plus installers
by Nathaniel Echols 23 Sep '14

23 Sep '14

Hi all-- We now have improved installers for CCTBX with all optional third-party dependencies, including numpy, wxPython, and matplotlib; these are basically just a simplified Phenix installer (minus anything that isn't open-source, obviously). For anyone doing visualization these are probably preferable to the default packages. More useful for doing active development is that since these include the pre-build Python, if you are working directly with the CCTBX sources you can bootstrap from these packages. Yesterday's build is here: http://cci.lbl.gov/cctbx_build/plus_bundles/2014_09_08_0005/ and in general the latest version can be obtained here: http://cci.lbl.gov/cctbx_build/plus_bundles/current although today's build isn't finished yet. The next build will also incorporate IPython. I still need to fix the download page so these are listed alongside the old bundles. Once this is done we'll probably declare an official "release". -Nat

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Tests which randomly pass or fail (nag)
by Graeme.Winter＠diamond.ac.uk 16 Sep '14

16 Sep '14

Hi Folks Quick nag if I may... if people have tests which employ random inputs (e.g. random unit cell, random amplitudes and phases) please could they set a seed or select from some seeds which should give random values which work, or fix their tests so that all random values work (ideally!) That way when tests fail people know something is wrong, rather than everything is fine but the random values drawn are troublesome... Sorry for sounding grumpy! Cheerio Graeme -- 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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order bias in flex.random_permutation
by Keitaro Yamashita 11 Sep '14

11 Sep '14

Dear cctbx developers, I happened to notice that the implementation of flex.random_permutation (scitbx/random.h) results in biased order because each element is always swapped with the element randomly selected from entire range of array. For details, please see the second paragraph and the right figure of http://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle#Implementation_er… I reproduced the plot using flex.random_permutation. Actually this seems to have less impact because flex.random_permutation is rarely used in cctbx or phenix as far as I know. If needed, I would commit the corrected version (using the algorithm in the wikipedia article above). Best regards, Keitaro

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IPython with cctbx
by Oliver Zeldin 09 Sep '14

09 Sep '14

Dear Devs, Has anyone tried to get IPython working with cctbx? I'd really like to be able to use IPython notebooks for examples/tutorials/documented experiments, and was wondering if anyone else had thought the same thing. Cheers, Oli

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Re: [cctbxbb] Sphinx docs for CCTBX
by Nigel Moriarty 20 Aug '14

20 Aug '14

These links don't work for me. On Mon, Aug 18, 2014 at 3:16 PM, Ian Rees <irees(a)lbl.gov> wrote: > I'm using a separate build configuration for the docs. You can view > the nightly results here: > > http://cci-vm-6.lbl.gov:8010/builders/cctbx%2Bdocs-linux-64 > > If you click the first build, you can view the log files for each > step, and view the Sphinx log file by clicking "docs:cctbx stdio", > e.g. > > > http://cci-vm-6.lbl.gov:8010/builders/cctbx%2Bdocs-linux-64/builds/6/steps/… > > I'm working through the warnings now. Mostly missing references and > import errors. > > Ian > > On Fri, Aug 15, 2014 at 8:37 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > > On Fri, Aug 15, 2014 at 8:06 AM, Richard Gildea <rgildea(a)gmail.com> > wrote: > >> > >> I had a go at starting to document cctbx.uctbx.unit_cell, which as you > >> know is mainly a Boost.Python extension > >> (https://sourceforge.net/p/cctbx/code/20467/). Before I travel too much > >> further down this route, is this an appropriate way of documenting > >> Boost.Python extensions or is there a better way we can do this? > > > > > > I haven't had enough time to experiment to decide on the best approach. > I > > see three choices - the first is what you've done: > > > > class my_class (ext.my_class) : > > """doc""" > > > > def boosted_function (self, some_argument) : > > """function doc""" > > super(ext.my_class, self).boosted_function(some_argument) > > > > OR (2): > > > > ext.my_class.__doc__ = """doc""" > > ext.my_class.boosted_function.__func__.__doc__ = """function doc""" > > > > OR (3): > > > > put the docstrings in C++ code, for instance: > > > > .def("boosted_function", &my_class::boosted_function, "function doc") > > > > (not sure what the equivalent is for classes but it's probably pretty > > similar) > > > > My opinion is that (1) is much too prone to confusion and API conflicts > > unless we're already using this code structure (and FYI, you broke the > call > > signatures for a couple of methods). (3) is just gross. (2) is also > gross > > but has the virtue of being the least likely to break, and doesn't > require > > modifying C++ files. So I'm inclined to take that approach > > > > (For what it's worth, when modifying a class using the boost.python > > injector, we appear to be able to set __doc__ inside there; see > > iotbx.pdb.hierarchy for an example.) > > > >> It would be good to get the documentation for the core cctbx classes up > >> and running, however several of the core classes (e.g. > >> cctbx.sgtbx.space_group, cctbx.uctbx.unit_cell, flex arrays) are mostly > >> Boost.Python extensions, so it would be good to arrive at a sensible > way to > >> document these extensions. > > > > > > Agreed. I think for flex arrays we will be stuck writing the docstrings > in > > C++ - however since these are relatively stable APIs it should be > reasonably > > straightforward. > > > > -Nat > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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real-space symmetry operators
by Nathaniel Echols 18 Aug '14

18 Aug '14

Hi all-- I'm trying to figure out how to orthogonalize symmetry operators given a unit cell, which doesn't seem to be something we have code for. These appear in PDB files in the REMARK 290 section but I haven't been able to find any other software that generates them, and the relationship between the symops and the real-space equivalents is unclear. I assume this is conceptually similar to orthogonalizing fractional coordinates, but unit_cell.orthogonalize() does not quite do what I wanted. In the PDB, for P63 it has this (excerpted): REMARK 290 2555 -Y,X-Y,Z ... REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 which looks like it should be relatively straightforward, but I'm not very good with matrices. Does anyone know the correct math for this? The corresponding rt_mx object from sgtbx looks like this: r=(0.0, -1.0, 0.0, 1.0, -1.0, 0.0, 0.0, 0.0, 1.0) t=(0.0, 0.0, 0.0) (Yes, I realize that there are much easier ways to apply symmetry operators to coordinates, but I want to limit the number of matrix multiplications involved when starting from Cartesian coordinates.) thanks, Nat

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Sphinx docs for CCTBX
by Nathaniel Echols 15 Aug '14

15 Aug '14

Thanks to some superb work by Nader Morshed, Oliver Zeldin, and Ian Rees, we now have automatically updated Sphinx docs for CCTBX: http://cci.lbl.gov/cctbx_docs/ Obviously these are still pretty sparse - right now most of the formal documentation is clustered here: libtbx libtbx.utils libtbx.phil (mostly re-using Ralf's old documentation) cctbx.miller iotbx.pdb (built on Ralf's newsletter article) mmtbx.command_line These are a combination of inline docstrings and separate restructured text files in cctbx_project/sphinx. We have automatically generated rst files for some modules, but others will need to be added manually. In the end I think we'll want to curate every file, but the current layout will get us started. To facilitate additional contributions, I've modifed the installation script for base packages to include a --sphinx option. After setting up CCTBX you can then do this: cd $BUILD libtbx.configure sphinx cd $SRC/cctbx_project/sphinx make html and you will get the full documentation built locally. I am still figuring out how to use Sphinx effectively; it is definitely possible to document Boost.Python extensions but it's not quite as obvious. I don't expect us to retroactively document several hundred thousand lines of code written over a decade, but if we can get the core parts thoroughly covered that will greatly reduce the barrier for new developers. Suggestions for particular modules to focus on are appreciated; I am going to try to cover the basic PDB+reflection file functionality. I encourage anyone doing CCTBX-related development to contribute as you go. (They don't need to be your own APIs, just modules you're reasonably familiar with.) Those of you who already have a ton of undocumented code can expect me to harass you periodically about fixing this. (Note that I've cannibalized at least one newsletter article for this, and continue to do so; we should re-use existing prose descriptions as much as possible without violating copyrights.) -Nat

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Re: [cctbxbb] resend
by Mustyakimov, Marat 24 Jul '14

24 Jul '14

Loop through symops: apply each symop to the original asu, then apply unit translations to minimize its distance to the original asu, test if new asu intersects with the target 27-bricks-large box, use it, if it does. Keep in mind that asu is not always a brick, it is always a convex polyhedron in cctbx. I do not see any good reason for doing all that. I do not read cctbxbb. On Jul 24, 2014, at 2:43 PM, Alastair Fyfe <afyfe(a)soe.ucsc.edu> wrote: >> Hi Marat, my apologies if this is a duplicate. From Pavel's comment it occurred to me you might not follow posts to the cctxbb >> Alastair >> ------ >> >> Many thanks for your replies. >> >> Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results >> back to unit cell thus obtaining a "full" unit cell (I expect >> "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap >> with the 26-brick neighborhood of the starting brick. This should work >> but seems inefficient. >> >> Marat: applying SymOps to the basis vectors seems a great idea. >> However, it wasn't clear to me how to combine sg SymOps to yield the >> 26 adjacent bricks. Does the map expansion code do this? >> >> >

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Re: [cctbxbb] 26-fold symm expansion of asu?
by Alastair Fyfe 24 Jul '14

24 Jul '14

Many thanks for your replies. Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results back to unit cell thus obtaining a "full" unit cell (I expect "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap with the 26-brick neighborhood of the starting brick. This should work but seems inefficient. Marat: applying SymOps to the basis vectors seems a great idea. However, it wasn't clear to me how to combine sg SymOps to yield the 26 adjacent bricks. Does the map expansion code do this? On 07/23/2014 12:00 PM, cctbxbb-request(a)phenix-online.org wrote: > Send cctbxbb mailing list submissions to > cctbxbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/cctbxbb > or, via email, send a message with subject or body 'help' to > cctbxbb-request(a)phenix-online.org > > You can reach the person managing the list at > cctbxbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cctbxbb digest..." > > > Today's Topics: > > 1. Re: 26-fold symm expansion of asu? (Pavel Afonine) > 2. Re: 26-fold symm expansion of asu? (Mustyakimov, Marat) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Jul 2014 18:58:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Cc: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <53CF16C8.5040504(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you > want and probably that would be what you call "slow". Could you please > explain some more what it is for and why, and may be give some context? > Perhaps that helps me to see if we have something similar already > available.. > > For instance we have very efficient code that computes maps in ASU, and > also that expands map in ASU into the whole P1 box. This is something > Marat wrote recently and is very efficient. May be you can reuse that or > at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: >> Hi, >> I'd be grateful for any pointers to clipper or cctbx code that >> addresses the following: given a "brick" of map grid coordinates that >> enclose the asu, obtain the 26 symmetry-related "bricks" which contact >> it. Calculating this by successively generating symmetry mates and >> testing seems slow; I was wondering whether there was a better way. >> thank you, >> Alastair Fyfe >> UCSC >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Jul 2014 14:01:13 +0000 > From: "Mustyakimov, Marat" <mustyakimovm(a)ornl.gov> > To: Pavel Afonine <pafonine(a)lbl.gov> > Cc: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] 26-fold symm expansion of asu? > Message-ID: <9457BEEC-4821-4BBB-8D91-E903AAFAE7F0(a)ornl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > The fast way to generate symmetry equivalent ASU: > Apply symmetry operation to unit vectors: ex = SymOp*(1,0,0), ey=SymOp*(0,1,0) and ez=SymOp*(0,0,1); > Then every map point of the symmetry related asu is obtained from the original one: > new_ijk = i*ex + j*ey + k*ez where (i,j,k) is the grid point in the original ASU. > > Marat Mustyakimov > P.O. Box 2008, Bldg. 8600, MS-6475 > Oak Ridge National Lab > Oak Ridge TN 37831 USA > e-mail: mustyakimovm(a)ornl.gov<mailto:[email protected]> > e-mail: marat.mustyakimov(a)gmail.com<mailto:[email protected]> > Tel: +1-865-253-3924 > > On Jul 22, 2014, at 9:58 PM, Pavel Afonine <pafonine(a)lbl.gov<mailto:[email protected]>> wrote: > > Hi Alastair, > > I think I can write a piece of code using cctbx that would do what you want and probably that would be what you call "slow". Could you please explain some more what it is for and why, and may be give some context? Perhaps that helps me to see if we have something similar already available.. > > For instance we have very efficient code that computes maps in ASU, and also that expands map in ASU into the whole P1 box. This is something Marat wrote recently and is very efficient. May be you can reuse that or at least harvest ideas? > > I'm copying to Marat in case he has comments. > > Pavel > > On 7/21/14, 2:14 PM, Alastair Fyfe wrote: > Hi, > I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. > thank you, > Alastair Fyfe > UCSC > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > ------------------------------ > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > > End of cctbxbb Digest, Vol 64, Issue 2 > **************************************

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