- cctbxbb - phenix-online.org

crystal packing/unit cell question
by Jessica Grant 09 Nov '11

09 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

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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

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CCTBX comprehensive overview
by Graeme.Winter＠Diamond.ac.uk 13 Oct '11

13 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

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cropping out a fragment
by Monarin Uervirojnangkoorn 05 Oct '11

05 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

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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

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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

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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

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Bug in structure.expand_to_p1?
by Jan Marten Simons 22 Jun '11

22 Jun '11

Hi, I'm quite puzzled at the moment. using this code: if __name__ == '__main__': quartz_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.01,5.01,5.47,90,90,120), space_group_symbol="P6222")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(1/2.,1/2.,1/3.), u=0.2), xray.scatterer( label="O", site=(0.197,-0.197,0.83333), u=0)])) ref_structure = quartz_structure.expand_to_p1( append_number_to_labels=True) print(ref_structure.as_py_code()) I get this result: xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(5.01, 5.01, 5.47, 90, 90, 120), space_group_symbol="P 1"), scatterers=flex.xray_scatterer([ xray.scatterer( #0 label="Si_0", site=(0.500000, 0.500000, 0.333333), u=0.200000), xray.scatterer( #1 label="Si_1", site=(0.000000, 0.500000, 0.666667), u=0.200000), xray.scatterer( #2 label="Si_2", site=(0.500000, 0.000000, 1.000000), u=0.200000), xray.scatterer( #3 label="O_0", site=(0.197000, -0.197000, 0.833333), u=0.000000), xray.scatterer( #4 label="O_1", site=(0.394000, 0.197000, 1.166667), u=0.000000), xray.scatterer( #5 label="O_2", site=(-0.197000, -0.394000, 1.500000), u=0.000000), xray.scatterer( #6 label="O_3", site=(0.197000, 0.394000, 1.500000), u=0.000000), xray.scatterer( #7 label="O_4", site=(-0.394000, -0.197000, 1.166667), u=0.000000), xray.scatterer( #8 label="O_5", site=(-0.197000, 0.197000, 0.833333), u=0.000000)])) It bothers me that there are x,y,z not in [0, 1[. Shouldn't the newly expanded cell only contain atoms within the unit cell? I realize, that the quarz structure (from the sample code from the website) also violates this with Oy beeing negative, but still I think expand_to_p1 should return a regular structure. Also is there a method already implemented to change a structure from a non- conventional description into a conventional one (with all atoms within its unit cell)? With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University

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CCTBX for Debian + PATCH
by Radostan Riedel 14 Jun '11

14 Jun '11

Hello, I'm about to make a (multi binary) Debian source package of CCTBX-Project. The plan is to build a few small Packages that depends on each other. So the python stuff would go to /usr/lib/python*.*/dist-packages/ and the libraries would go to /usr/lib and the Headers to /usr/include. Example: ''' python-iotbx: installs iotbx python module and extensions to /usr/lib/python*.*/dist-packages/ libcctbx0: installs libcctbx.so.0 etc. to /usr/lib/ libcctbx-dev: installs a symlink libcctbx.so ---> libcctbx.so.0 etc. and header files to /usr/include/cctbx ''' This would follow strictly the Debian Policy, so maybe when this will be accepted we could see CCTBX in the official Repos of Debian and Ubuntu etc. But for that I still have a few problems: 1.) The SONAME and SOVERSION is missing from the shared libraries. I'm attaching a patch that can fix this for GNU/Linux. That produces files like this: ''' ls lib/libcctbx* lib/libcctbx_sgtbx_asu.so lib/libcctbx_sgtbx_asu.so.0 lib/libcctbx.so lib/libcctbx.so.0 ''' 2.) PyCifRW: I had to remove it from the sources because it ain't free software because of some lines in their license. It wasn't accepted to Fedora because of that, so I guess I can forget Debian either. 3.) In your changelog I read you wanna get rid of the "from __future__ import division" and change to "python -Qnew". This would be a problem for me, because than I couldn't use it from sys.path anymore. I have a Django project at work that imports some cctbx modules directly from pythonpath. And I can't really call "cctbx.python" for that, otherwise I would have to patch my Apache and mod_wsgi, respectively cctbx. Wouldn't it be better to install all python modules to the standard python location of the Distribution than making dispatchers with hardcoded paths? Also, when the libraries, headers and python stuff would be in their standard location, everyone could just import it from anywhere? I will be finished soon with packaging and then I will upload it to my PPA on Lauchpad https://launchpad.net/~raybuntu/+archive/xray which is empty by now. And I think this could also be adopted to other Distributions like Fedora. I'd be glad to hear some critical opinions about this from you. regards R.R.

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Best way to do 3d xyz plots with cctbx?
by Jan Marten Simons 08 Jun '11

08 Jun '11

Hi, I noticed cctbx has some custom wx based graphic windows to display various specialized plots and visualisations. I'm interested in generating some simple 3d xyz plots like in [1]. Is functionality for this included in cctbx or should I rather use another python based plotter for this? [1] http://pyx.sourceforge.net/examples/3dgraphs/surface.html Thanks in advance, Jan

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