- cctbxbb - phenix-online.org

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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