- cctbxbb - phenix-online.org

Problems building scitbx.random
by Jan Marten Simons 29 Nov '11

29 Nov '11

Hi, After doing a fresh checkout with these commands: > #! /bin/csh -fe > set verbose > curl http://cci.lbl.gov/cctbx_build/results/current/cctbx_bundle.selfx -o cctbx_bundle.selfx > perl cctbx_bundle.selfx 0 > rm cctbx_bundle.selfx > rm cctbx_install_script.csh > mv cctbx_sources sources > cd sources > svn co https://cctbx.svn.sourceforge.net/svnroot/cctbx/trunk cctbx_project > cctbx_project/libtbx/development/move_obsolete_from_bundle.csh And using these commands to configue and build cctbx: > mkdir -p build > cd build > python ../sources/cctbx_project/libtbx/configure.py -- enable_openmp_if_possible=True --scan_boost --build=release boost_adaptbx cctbx chiltbx crys3d iotbx mmtbx rstbx ucif smtbx clipper_adaptbx fable scitbx > source setpaths.sh > make || ( echo "Make failed!"; exit 1 ) I encounter these errors: Processing: "/home/mu/cctbx/cctbx- dev/sources/cctbx_project/crys3d/libtbx_refresh.py" Traceback (most recent call last): File "../sources/cctbx_project/libtbx/configure.py", line 21, in <module> run() File "../sources/cctbx_project/libtbx/configure.py", line 17, in run libtbx.env_config.cold_start(sys.argv) File "/home/marten/cctbx/cctbx- dev/sources/cctbx_project/libtbx/env_config.py", line 2061, in cold_start env.refresh() File "/home/mu/cctbx/cctbx-dev/sources/cctbx_project/libtbx/env_config.py", line 1401, in refresh module.process_libtbx_refresh_py() File "/home/mu/cctbx/cctbx-dev/sources/cctbx_project/libtbx/env_config.py", line 1678, in process_libtbx_refresh_py execfile(abs(custom_refresh), {}, {"self": self}) File "/home/mu/cctbx/cctbx- dev/sources/cctbx_project/crys3d/libtbx_refresh.py", line 3, in <module> from crys3d import qttbx File "/home/mu/cctbx/cctbx- dev/sources/cctbx_project/crys3d/qttbx/__init__.py", line 4, in <module> import gltbx.util File "/home/mu/cctbx/cctbx-dev/sources/cctbx_project/gltbx/util.py", line 1, in <module> import scitbx.array_family.flex # import dependency File "/home/mu/cctbx/cctbx- dev/sources/cctbx_project/scitbx/array_family/flex.py", line 10, in <module> import scitbx.random File "/home/mu/cctbx/cctbx- dev/sources/cctbx_project/scitbx/random/__init__.py", line 24, in <module> mt19937 = mersenne_twister_19937(value=get_random_seed()) NameError: name 'mersenne_twister_19937' is not defined To me these look like scitbx.random-ext is not built. Is this a regression from the changes to the build system or am I doining something wrong here? Cheers, Jan

2 3

Using cctbx as a C++ only library
by Martin Uhrin 26 Nov '11

26 Nov '11

Dear Cctbx community, thank you very much for the great library, full of wonderful algorithms. I'm writing a structure searching engine in C++ to be used as a high throughput method to do energy landscape sampling with a view to finding new ground state crystal structures. Key requirements of this project are efficiency and ease of development & deployment. Cctbx has many useful algorithms and data structures that I would like to avoid having to re-code if possible. Thus I've downloaded and played with the source as it is but have found it difficult to integrate with my project (for understandably reasons given the goals of cctbx). My main goals regarding ease of development & deployment mean that it would be very inconvenient to distribute the entire cctbx with my code. Ideally I'd like to achieve the following: * strip out everything python related (apart from maybe the build system) * strip out all modules (namespaces) that are unused by my code leaving a fairly bare-bones C++ library that is quick and easy to build. Is anyone able to comment on how feasible this might be? Is this even worth attempting? Many thanks, -Martin -- Martin Uhrin Tel: +44 207 679 3466 Department of Physics & Astronomy Fax:+44 207 679 0595 University College London martin.uhrin.10(a)ucl.ac.uk Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk

2 3

cctbx + PyPy?
by Jan Marten Simons 25 Nov '11

25 Nov '11

Hi, PyPy 1.7 was released just a few days ago: http://morepypy.blogspot.com/2011/11/pypy-17-widening-sweet-spot.html After taking a look at http://speed.pypy.org/ I'm wondering if it would be possible to get cctbx to work with PyPy-jit instead of CPython. Perhaps it's a little bit early, as they are still working on a complete numpy integration and I'm not sure how well boost.python fits into this. But in general speeding up the python parts looks nice if one does not have to invest too much time into this. Has any of you already done some tests with PyPy? Cheers, Jan

2 1

crystal packing/unit cell question
by Jessica Grant 08 Nov '11

08 Nov '11

I am new to cctbx and crystallography in general. I am trying to take a pdb file and produce a representation of the crystal, similar to the symmetry mates produced in pymol. I have used cctbx to apply the symmetry operators, but this gives atomic coordinates that are quite spread out. I think what I want to do is to fill the unit cell, or in some way extract crystal packing information. I would like, in the end, to be able to build files with a physically realistic representation of different sized crystals, so I can go on to study the interactions of molecules within those crystals. Is there a way to do this in cctbx? Thanks! Jessica

5 11

flex index
by Monarin Uervirojnangkoorn 18 Oct '11

18 Oct '11

Hi, I'm using flex and 'd like to get an access to elements fall beyond/ below certain value. eg. a=[1,4,5,7,5,6,6,1] anything beyond 5 should be set to 5. (in matlab then a(a>5)=5;) if you could tell me how to do this quickly for flex, that would be great. for now i use loop and that is... pretty slow. many thanks. mona ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ Institute of Biochemistry, Institut für Neuro- und Bioinformatik, Graduate School for Computing in Medicine and Life Sciences University of Lübeck, Ratzeburger Allee 160 Lübeck 23538 Germany Tel: +49451-5004072 Fax: +49451-5004068

2 3

CCTBX comprehensive overview
by Graeme.Winter＠Diamond.ac.uk 12 Oct '11

12 Oct '11

Hi Folks, Is there somewhere a comprehensive overview of what is available within cctbx? I have had a request for this from someone who may be interested in using it, but does not want to start looking until they know what is in there, without inspecting any code. Specifically, an idea of what is available from Python would hit the spot. Is there a way to generate this or does it already exist on the web? Thanks in advance, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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

cropping out a fragment
by Monarin Uervirojnangkoorn 04 Oct '11

04 Oct '11

Hi all, I'd like to crop out a portion of a fragment (say a helix) from real_map by specifying fractional coordinates. would be nice to know if there is any specific routine for this. (oh .. & ++ option like crop only 2 angstroms from the location of the atom would be really nice). thankx Best, Mona ~.~.~.~><~.~~.~.~. Institute of Biochemistry, Institut of Neuro- and Bioinformatics Graduate School for Computing in Medicine and Life Sciences University of Lübeck, Ratzeburger Allee 160 Lübeck 23538 Germany

2 1

Deleting batch from mtz batch header via iotbx.mtz
by Graeme.Winter＠Diamond.ac.uk 27 Sep '11

27 Sep '11

Hi Folks, Is there a way to delete a batch from an mtz file batch header? Been trying to do this and it looks like it is impossible - though you can add batches. Clearly there is the worry that the subsequent batch column may then refer to a missing batch, however... it would be handy to be able to do this (providing that the reflections were also removed elsewhere in the calling code) Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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 5

Lattice options & changes of basis
by Graeme.Winter＠Diamond.ac.uk 20 Sep '11

20 Sep '11

Hi Folks, I have a very simple question which I *know* can be done with cctbx, using the Python API, but I cannot for the life of me figure out how to do it. I have even read the code, it's just not clear. I have a Bravais lattice and cell, say oP and 20, 30, 40, 90, 90, 90 - what I would like back is a list of pointgroup, cell, reindexing operation for all compatible unique settings i.e. 1 x P1, 3 x P2, 1 x P222 - from a Python loop. At the moment I run iotbx.lattice symmetry and grep the results, which is not a great idea. It would also be useful to give the reindex operations to centred lattices. I have also stared at phenix.explore_metric_symmetry and remain puzzled despite my attempt to essentially duplicate the code. I just can't get the reindex operation out. Has anyone some simple code to do this? I tried piggybacking on pointgroup tools but that did not lead to enlightenment. I suspect using elementary ish operations would be better... Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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

3 3

Conversion from symmetry operation to matrix
by Graeme.Winter＠Diamond.ac.uk 13 Jul '11

13 Jul '11

Dear All, For a little while now I have been using some cctbx jiffy code to convert from symmetry operations to matrices to help with testing reindexing data. This works as def symop_to_mat(symop): return matrix.sqr(sgtbx.rt_mx( sgtbx.parse_string(symop)).as_double_array()[:9]).transpose().elems Which is plenty simple. However it just exploded when given "1/2*z,-y+1/2*z,x" - reasonably really as this is not a rotation. It is however a valid reindexing operation to go from C2 to P1. Does anyone have code which will handle this general transformation from a reindexing operation to a matrix, which will cope with the fact that the resulting matrix is not RT? I had a little jiffy I wrote using ccp4f lib (symop2mat - you can probably see it!) but I am trying to do away with things like that and do everything properly... Many thanks in advance, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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

4 6