- cctbxbb - phenix-online.org

Moving cctbx to git
by markus.gerstel＠diamond.ac.uk 24 Nov '16

24 Nov '16

Hello everyone, As Aaron requested - here is an update regarding the move to GitHub. At this time if you want to commit code: *keep committing to Sourceforge*. Do not worry about leaving uncommitted changes in your SVN tree. Those can be migrated later. The Sourceforge cctbx repository history has now been migrated to GitHub. The repository lives at https://github.com/cctbx/cctbx. Please do not commit to this repository yet! Over the next few days the bootstrap script will be modified alongside the build servers to point to the GitHub repository. This means there will only be limited testing, and the produced builds will lag behind the development effort. To be listed as a developer on https://github.com/cctbx you need to set your visibility to public at https://github.com/orgs/cctbx/people<%20https:/github.com/orgs/cctbx/people>. You can also view some fancy graphs about the cctbx project history at https://github.com/cctbx/cctbx/graphs/contributors<%20https:/github.com/cctbx/cctbx/graphs/contributors> If you haven't done it before, now is a good time to set up your local installation of git to use your name and mail address with git config --global user.name "John Doe" git config --global user.email your_email(a)example.com<mailto:[email protected]> as well as this setting to avoid merge commits: git config --global pull.rebase true Note that you must set these on every computer you use! You may want to keep a copy of those commands around in case you ever get a new computer. You should use mail addresses registered with your github account, or - if you enable it in your github account - the anonymous address offered by github. You may want to use the time to sort out your ssh access keys with your GitHub account, and play around with git a bit. You can test that everything works using the temporary sandbox repository of cctbx. Here are some commands to get you started: git clone [email protected]:cctbx/cctbx-playground.git cd cctbx-playground echo some text >> some-file git add some-file git commit -m "some commit" git push git log Then go to https://github.com/cctbx/cctbx-playground/commits/master to see how other people will see your commits. The next steps: *Tuesday 8th November 2016, 11:59pm Pacific Time* *= Wednesday 9th November 2016, 07:59am GMT:* Sourceforge: Committing allowed. GitHub: Checkout/Cloning allowed, *Read-only*. We will update our build servers and the bootstrap script to refer to the git repositories. All commits still run into Sourceforge, and will be copied over to GitHub automatically every couple of hours. Since the build servers will only see code on GitHub, testing and deployment will be limited during this period. *Tuesday 22nd November 2016, 11:59pm Pacific Time* *= Wednesday 23rd November 2016, 07:59am GMT:* Sourceforge: *Read-only*. GitHub: Committing allowed We should have achieved a stable build on both Jenkins and Buildbot by this time. Change any website pointers from SF to GitHub. Instructions to migrate local developer repositories will be sent around. All future commits should go to GitHub only. Remaining commits on Sourceforge will be migrated to GitHub. -Markus Dr Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- 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

5 8

Re: [cctbxbb] cctbxbb Digest, Vol 92, Issue 17
by Tijskens Engelbert 22 Nov '16

22 Nov '16

> Message: 2 > Date: Mon, 21 Nov 2016 13:22:20 +0000 > From: Gabor Bunkoczi <gabor.bunkoczi(a)googlemail.com> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] convert an arbitrary point to one inside the > asymmetric unit > Message-ID: > <CABYxhoWJgnRWL0Tun6M9MzcQAWNfy77YMNRSqEw+L4_b5yFkvA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Engelbert, > > you can use the asu_mappings objects to compute this (there may be > something more suitable for regular grids). Here is a link to a tutorial > written by Ralf Grosse-Kunstleve, where this is explained: > > http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf > > BW, Gabor I have looked into this, but if i understand it well, it does exactly the opposite of what i want: it extends the asymmetric unit to a spherical region and makes symmetric copies of some specified points in the (scatterers in the tutorial mentioned). i have points outside the asymmetric unit, and i want to find the corresponding points inside the asymmetric unit from which i can interpolate the electron density. kindest regards and still hoping … bert

2 1

convert an arbitrary point to one inside the asymmetric unit
by Tijskens Engelbert 22 Nov '16

22 Nov '16

Hi, I am an experienced C++ and Python programmer, but new to cctbx. Can any tell me if there is an algorithm in cctbx available to convert an arbritrary point in direct space to the corresponding point in the asymmetric unit of a given space group? i can figure out how to convert it to the corresponding point in the unit cell at the origin, but from there to the asymmetric unit is unclear to me. I found the brick class which gives me the assymmetric unit from cctbx import crystal,sgtbx if __name__=='__main__': crystal_symmetry = crystal.symmetry( unit_cell=(3.5093,3.5093,3.5093,90,90,90) , space_group_symbol="229" # = "I m -3 m" ) sg = crystal_symmetry.space_group() brick = sgtbx.brick( sg.type() ) print brick I also found cctbx::sgtbx::asu and the classes therein, but they are largely undocumented. For the interested, this is the problem i want to solve: I have a (scalar) physical property P(r), depending on spatial position, presented as a 3D array on a regular grid over the unit cell (space group is known). I need to integrate P(r)*f(r), f(r) being an arbitrary function over a region of direct space, which typically comprises several unit cells. In order to reduce the memory footprint of the P array, i would like to restrict it to the space group’s asymmetric unit. All help is greatly appreciated. kindest regards, Dr [Engel]bert Tijskens HPC Analyst/Consultant Flemish Supercomputer Center vscentrum.be<http://vscentrum.be> HPC core facility CalcUA uantwerp.be/calcua<http://uantwerp.be/calcua> Computational mathematics www.uantwerpen.be/en/rg/cma<http://www.uantwerpen.be/en/rg/cma> University of Antwerp Middelheimlaan1 G.309, B-2020 Antwerp, Belgium engelbert.tijskens(a)uantwerpen.be<mailto:[email protected]> ++32 3 265 3879

3 3

Re: [cctbxbb] cctbxbb Digest, Vol 92, Issue 17
by Tijskens Engelbert 22 Nov '16

22 Nov '16

> Message: 3 > Date: Mon, 21 Nov 2016 13:38:21 +0000 > From: Gabor Bunkoczi <gabor.bunkoczi(a)googlemail.com> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] convert an arbitrary point to one inside the > asymmetric unit > Message-ID: > <CABYxhoUxqFsc0f_TjWwn4oC4hKFk8AEbzwx5=9=_+gwW3xmkpg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On second thought, the simplest solution is to use the direct_space_asu > object. This is available for all space groups: > >>>> from cctbx import sgtbx >>>> sgi = sgtbx.space_group_info( "P2" ) >>>> asu = sgi.direct_space_asu() >>>> asu.is_inside( ( 0, 0, 0 ) ) > True >>>> asu.is_inside( (0, 0, 0.51 ) ) > False > > BW, Gabor > Thanks for your quick reply, Gabor. Unfortunately, it does not solve my question. For the example you give above, the second point is not inside the asu, and my question is how i can the corresponding point inside the asu, For a simple space group as P2 the answer is easily figured out by hand. For a space group such as I m -3 m, it becomes complicated. I would like to have a (computationally efficient) method for finding the point inside the asu given an arbitrary point which works for every space group. Any “third” thoughts? kindest regards, bert

2 1

Re: [cctbxbb] Unstable platform-dependent sort order for flex.sort_permutation
by richard.gildea＠diamond.ac.uk 21 Nov '16

21 Nov '16

Hi Oleg, The permutations would lead to the same sequence of miller indices, but in the context of an unmerged reflection array (i.e. miller.array.sort_permutation), then the data associated with those miller indices would not necessarily be in the same order. As the dataset is then split into two half-datasets, this difference in sort order leads to a different value of the calculate correlation coefficient between those two half datasets: https://github.com/cctbx/cctbx_project/blob/master/cctbx/miller/__init__.py… Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of oleg(a)olexsys.org [oleg(a)olexsys.org] Sent: 18 November 2016 15:59 To: cctbx mailing list Subject: Re: [cctbxbb] Unstable platform-dependent sort order for flex.sort_permutation Hi Richard, it is a bug only if the permutations do not lead to the same sequence. Otherwise you cannot expect to get the same sorting permutations for collections with redundant data on different platforms or even between different versions of compilers. Cheers, Oleg. ________________________________ From: cctbxbb-bounces(a)phenix-online.org <cctbxbb-bounces(a)phenix-online.org> on behalf of richard.gildea(a)diamond.ac.uk <richard.gildea(a)diamond.ac.uk> Sent: 18 November 2016 14:12:29 To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] Unstable platform-dependent sort order for flex.sort_permutation Hi, I've been trying to diagnose why the miller array cc_anom calculations seem to be platform dependent. I've narrowed this down to a variation in the sort order returned by flex.sort_permutation which is called from within miller.array.sort("packed_indices"). The following code demonstrates the problem and the different output I get on mac and Linux: Mac: >>> from scitbx.array_family import flex >>> a = flex.size_t([7, 1, 1, 5, 1, 3, 3, 7, 1, 7, 3, 3, 5, 7, 5, 5, 5, 1, 1, 1]) >>> print list(flex.sort_permutation(a)) [1, 2, 4, 8, 17, 18, 19, 5, 6, 10, 11, 3, 12, 14, 15, 16, 0, 7, 9, 13] Linux: >>> from scitbx.array_family import flex >>> a = flex.size_t([7, 1, 1, 5, 1, 3, 3, 7, 1, 7, 3, 3, 5, 7, 5, 5, 5, 1, 1, 1]) >>> print list(flex.sort_permutation(a)) [19, 1, 2, 18, 4, 17, 8, 11, 10, 6, 5, 12, 14, 15, 16, 3, 9, 7, 13, 0] Is it known/expected for the sort order to be platform dependent, or is this a bug? Here is the relevant code for flex.sort_permutation(): https://github.com/cctbx/cctbx_project/blob/master/scitbx/array_family/sort… Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- 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 _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb

5 9

Unstable platform-dependent sort order for flex.sort_permutation
by richard.gildea＠diamond.ac.uk 19 Nov '16

19 Nov '16

Hi, I've been trying to diagnose why the miller array cc_anom calculations seem to be platform dependent. I've narrowed this down to a variation in the sort order returned by flex.sort_permutation which is called from within miller.array.sort("packed_indices"). The following code demonstrates the problem and the different output I get on mac and Linux: Mac: >>> from scitbx.array_family import flex >>> a = flex.size_t([7, 1, 1, 5, 1, 3, 3, 7, 1, 7, 3, 3, 5, 7, 5, 5, 5, 1, 1, 1]) >>> print list(flex.sort_permutation(a)) [1, 2, 4, 8, 17, 18, 19, 5, 6, 10, 11, 3, 12, 14, 15, 16, 0, 7, 9, 13] Linux: >>> from scitbx.array_family import flex >>> a = flex.size_t([7, 1, 1, 5, 1, 3, 3, 7, 1, 7, 3, 3, 5, 7, 5, 5, 5, 1, 1, 1]) >>> print list(flex.sort_permutation(a)) [19, 1, 2, 18, 4, 17, 8, 11, 10, 6, 5, 12, 14, 15, 16, 3, 9, 7, 13, 0] Is it known/expected for the sort order to be platform dependent, or is this a bug? Here is the relevant code for flex.sort_permutation(): https://github.com/cctbx/cctbx_project/blob/master/scitbx/array_family/sort… Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- 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 1

convert an arbitrary point to one inside the asymmetric unit
by Tijskens Engelbert 19 Nov '16

19 Nov '16

Hi, I am an experienced C++ and Python programmer, but new to cctbx. Can any tell me if there is an algorithm in cctbx available to convert an arbritrary point in direct space to the corresponding point in the asymmetric unit of a given space group? i can figure out how to convert it to the corresponding point in the unit cell at the origin, but from there to the asymmetric unit is unclear to me. I found the brick class which gives me the assymmetric unit from cctbx import crystal,sgtbx if __name__=='__main__': crystal_symmetry = crystal.symmetry( unit_cell=(3.5093,3.5093,3.5093,90,90,90) , space_group_symbol="229" # = "I m -3 m" ) sg = crystal_symmetry.space_group() brick = sgtbx.brick( sg.type() ) print brick I also found cctbx::sgtbx::asu and the classes therein, but they are largely undocumented. For the interested, this is the problem i want to solve: I have a (scalar) physical property P(r), depending on spatial position, presented as a 3D array on a regular grid over the unit cell (space group is known). I need to integrate P(r)*f(r), f(r) being an arbitrary function over a region of direct space, which typically comprises several unit cells. In order to reduce the memory footprint of the P array, i would like to restrict it to the space group’s asymmetric unit. All help is greatly appreciated. kindest regards, Dr [Engel]bert Tijskens HPC Analyst/Consultant Flemish Supercomputer Center vscentrum.be<http://vscentrum.be> HPC core facility CalcUA uantwerp.be/calcua<http://uantwerp.be/calcua> Computational mathematics www.uantwerpen.be/en/rg/cma<http://www.uantwerpen.be/en/rg/cma> University of Antwerp Middelheimlaan1 G.309, B-2020 Antwerp, Belgium engelbert.tijskens(a)uantwerpen.be<mailto:[email protected]> ++32 3 265 3879

1 0

who else has troubles to commit to cctbx now?
by Pavel Afonine 17 Nov '16

17 Nov '16

Can't commit anything since yesterday: pva_mbp:/Users/pafonine/phenix_dev/modules/cctbx_project/mmtbx % svn commit -m "test" maps/correlation.py Sending maps/correlation.py Transmitting file data .svn: E000013: Commit failed (details follow): svn: E000013: Can't create directory '/svn/p/cctbx/code/db/transactions/25717-1.txn': Permission denied pva_mbp:/Users/pafonine/phenix_dev/modules/cctbx_project/mmtbx % Nigel has the same issue. I don't see any warnings on sourceforge. Pavel

3 3

command line syntax for multiple scope PHIL
by R.D. Oeffner 10 Nov '16

10 Nov '16

Say a program, myprog, has a master PHIL definition like: minimization.input .multiple = True { file_name = None .type = str nval = None .type = int } and a PHIL input file like: minimization.input { file_name = experiment1.dat nval = 42 } minimization.input { file_name = experiment2.dat nval = 13 } so that the user on the command line can type "myprog phil_input.txt" What would be the equivalent command line syntax of the PHIL input above? Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 mobile: +44(0)7712 887162

2 2

Failing shelxl test
by Graeme.Winter＠diamond.ac.uk 10 Nov '16

10 Nov '16

Folks, I keep getting this error: libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py" P31 [FAIL] Time: 1.38 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 253, in <module> run(args=sys.argv[1:]) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 250, in run debug_utils.parse_options_loop_space_groups(args, run_call_back) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/debug_utils.py", line 120, in parse_options_loop_space_groups show_cpu_times, **kwds) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/debug_utils.py", line 83, in loop_space_groups call_back_result = call_back(flags, space_group_info, **kwds) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 244, in run_call_back verbose=flags.Verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 234, in exercise run_shelx(shelx_titl, structure_factors, verbose=verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 210, in run_shelx check_anisou(shelx_titl, xray_structure, shelx_pdb, verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 163, in check_anisou assert TotalMismatches == 0 AssertionError Please verify these tests manually. it is annoying as I understand it is to do with a change in shelxl - would it be OK to comment the test out to allow builds to pass? I am not sure it is useful at the moment Thank you 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

1 0