December 2014 - cctbxbb - phenix-online.org

dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

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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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