- cctbxbb - phenix-online.org

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

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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

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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 21 Jun '11

21 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 13 Jun '11

13 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 07 Jun '11

07 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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reflection conditions for non-standard settings
by David Waterman 06 Jun '11

06 Jun '11

Hi, I'm new to cctbx and to this mailing list, so please let me first apologise if the answer to this question should be obvious, or lies in the archive. I want a list of general reflection conditions for all space groups and settings listed in the CCP4 file syminfo.lib. At first I thought I could get this information from the online version of ITC vol A, but I soon realised that only certain standard settings are included. To avoid deriving them all by hand from the symop and cenop lines, I wonder if there is a foolproof way I can get this information from cctbx, but I don't know where to begin. Perhaps something in sgtbx? Many thanks -- David

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Introducing arbitrary translations in symmetry operations
by Emre S. Tasci 03 Jun '11

03 Jun '11

Dear All, We are trying to identify affine normalizers' space group from the additional operators, but having difficulties in introducing the arbitrary translations. As an example, suppose that our "base" space group is 25, and the additional operators are: -x,-y,-z x+1/2,y,z x,y+1/2,z x,y,z+t which, combined, defines P1 mmm But we couldn't find a way to introduce "x,y,z+t" while we are "expand_smx"ing the space group with these operators. Any ideas how to do this? With my thanks in advance, Emre -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Emre S. Tasci - http://www.emresururi.com Fisica de la Materia Condensada Facultad de Ciencia y Tecnologia Universidad del Pais Vasco Apartado 644 48080 Bilbao / Spain -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Re: [cctbxbb] Best way to compare incomplete f_hkl to calculated f_hkl
by Ralf W. Grosse-Kunstleve 11 Apr '11

11 Apr '11

Hi Jan, There are two steps to think about: .map_to_asu() and .common_set() or .common_sets(). Look for these methods in cctbx/regression/tst_miller.py, then add print statements to see how they work (run the command with e.g. "P31" so that it only exercisesone space group). However, the best way to compute f_calc given an array of f_obs is via f_calc = f_obs.structure_factors_from_scatterers( xray_structure).f_calc() This way the f_calc are directly compatible with the f_obs array. Ralf >________________________________ >From: Jan Marten Simons <marten(a)xtal.rwth-aachen.de> >To: cctbxbb(a)phenix-online.org >Sent: Monday, April 11, 2011 3:00 AM >Subject: Re: [cctbxbb] Best way to compare incomplete f_hkl to calculated f_hkl > >Hi, > >I'm looking at the best (=fastest) way to compare a (possibly incomplete) list >of observed reflections f_hkl_obs (or fo2_hkl_obs) to the f_hkl_calc of >calculated structure factors or intensities from a model structure. > >in miller.py there is a function to calculate a difference between f_obs and >f_calc, but it asserts that all reflections are present in f_obs: > >def f_obs_minus_f_calc(self, f_obs_factor, f_calc): >assert f_calc.is_complex_array() >assert self.indices().all_eq(f_calc.indices()) >assert self.anomalous_flag() is f_calc.anomalous_flag() >... > >In my case it's possible that some reflections could not be observed so they >should either be skipped or be assumed to be of zero intensity. As I could not >locate the definition for .all_eq(...), yet I'm not sure if this is already >handled and if it is how it is done. > >Then there is f_obs_minus_xray_structure_f_calc in miller.py as well. Would >this be a better approach if the model structure changes quite often? What if >I just got f_calc from another source (like doing some custom sped-up partial >structure factor calculation)? > >In general: What would be your advice on this with cctbx? > > >With regards, > >Dipl. Phys. > Jan M. Simons > >Institute of Crystallography >RWTH Aachen University >_______________________________________________ >cctbxbb mailing list >cctbxbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/cctbxbb > > >

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Best way to compare incomplete f_hkl to calculated f_hkl
by Jan Marten Simons 11 Apr '11

11 Apr '11

Hi, I'm looking at the best (=fastest) way to compare a (possibly incomplete) list of observed reflections f_hkl_obs (or fo2_hkl_obs) to the f_hkl_calc of calculated structure factors or intensities from a model structure. in miller.py there is a function to calculate a difference between f_obs and f_calc, but it asserts that all reflections are present in f_obs: def f_obs_minus_f_calc(self, f_obs_factor, f_calc): assert f_calc.is_complex_array() assert self.indices().all_eq(f_calc.indices()) assert self.anomalous_flag() is f_calc.anomalous_flag() ... In my case it's possible that some reflections could not be observed so they should either be skipped or be assumed to be of zero intensity. As I could not locate the definition for .all_eq(...), yet I'm not sure if this is already handled and if it is how it is done. Then there is f_obs_minus_xray_structure_f_calc in miller.py as well. Would this be a better approach if the model structure changes quite often? What if I just got f_calc from another source (like doing some custom sped-up partial structure factor calculation)? In general: What would be your advice on this with cctbx? With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University

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Use of cctbx with C++
by Flavio Zamponi 16 Mar '11

16 Mar '11

Hi all, I would like to use cctbx with C++. To start with I would like to do something basic, like: >/ from cctbx import xray />/ />/ xs = xray.structure.from_cif(file_path="my.cif") / I looked into the cctbx functions/class list, but I could not find something similar for C++. Can someone help me? Many thanks in advance, Flavio

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Docstrings and online reference
by Jan Marten Simons 10 Feb '11

10 Feb '11

Hi all, as you might have noticed I started to add some docstrings to functions. The purpose of those is to give a user of the toolbox an idea of this: 1. What's the purpose of the object (function/method/class/...)? 2. What objects should be thrown at it as input/keyword arguments? 3. What kind of object does one get as return value? I try to extract the information only from the source code, so it's possible that I sometimes don't get it right, as I'm just starting to explore the inner workings of the toolbox and esp. phenix related parts are (yet) quite obscure for me. I'm trying to document objects in a consistent way, so that a user (as well as ourself) doesn't get confused. I invite you all to adapt the scheme for new functions/objects you code and request comments on further improving it before extending its use, so that it's useful and to your likeing as well. A current example of one such docstring: def set_u_iso(self, value = None, values = None, selection = None): """Set isotropic mean thermic displacements of scatterers Input: value -- (optional) a single double value to set all u_iso of selected scatterers to values -- (optional) an array of double values to set all u_iso of selected scatterers to selection -- (optional) an array of bools to select scatterers to be updated with new u_iso values Returns: cctbx.xray.structure """ [...] During my first pass I noticed some already existing docstrings which are also shown in the online docs at e.g. http://cctbx.sourceforge.net/current/python/cctbx.xray.structure.html. Are those pages automatically generated via a cronjob or does it take a manual update to get this information up2date? Cheers, Jan

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Missing gaussians for some ions?
by Jan Marten Simons 23 Dec '10

23 Dec '10

Hi, I did some more tests using cif files from cod and found out that some of those trigger errors like this for http://www.crystallography.net/cif/1/1000029.cif: Traceback (most recent call last): File "Check_F_calc.py", line 29, in <module> f_calc = structure.structure_factors(d_min=1.0).f_calc() File "/home/marten/Arbeit/cctbx- latest/cctbx_sources/cctbx/xray/structure.py", line 813, in structure_factors algorithm=algorithm) File "/home/marten/Arbeit/cctbx- latest/cctbx_sources/cctbx/xray/structure_factors/from_scatterers.py", line 53, in __call__ miller_set=miller_set) File "/home/marten/Arbeit/cctbx- latest/cctbx_sources/cctbx/xray/structure_factors/from_scatterers_fft.py", line 32, in __init__ tolerance_positive_definite=manager.tolerance_positive_definite()) RuntimeError: gaussian not defined for scattering_type "Y4+". The cif file itself can be read and gives a valid summary: Number of scatterers: 13 At special positions: 5 Unit cell: (7.82927, 7.82927, 5.70757, 90, 90, 120) Space group: P 3 1 c (No. 159) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso Y1 Y4+ 2 ( 0.3333 0.6667 0.2420) 0.27 0.0000 [ - ] Si1 Si4+ 6 ( 0.5087 0.0819 0.2130) 0.77 0.0000 [ - ] Al1 Al3+ 6 ( 0.5087 0.0819 0.2130) 0.23 0.0000 [ - ] Si2 Si4+ 6 ( 0.1706 0.2533 0.0020) 0.77 0.0000 [ - ] Al2 Al3+ 6 ( 0.1706 0.2533 0.0020) 0.23 0.0000 [ - ] N1 N3- 2 ( 0.0000 0.0000 0.0000) 0.94 0.0000 [ - ] O1 O2- 2 ( 0.0000 0.0000 0.0000) 0.06 0.0000 [ - ] N2 N3- 2 ( 0.3333 0.6667 0.6530) 0.94 0.0000 [ - ] O2 O2- 2 ( 0.3333 0.6667 0.6530) 0.06 0.0000 [ - ] N3 N3- 6 ( 0.3458 -0.0472 -0.0050) 0.94 0.0000 [ - ] O3 O2- 6 ( 0.3458 -0.0472 -0.0050) 0.06 0.0000 [ - ] N4 N3- 6 ( 0.3219 0.3180 0.2460) 0.94 0.0000 [ - ] O4 O2- 6 ( 0.3219 0.3180 0.2460) 0.06 0.0000 [ - ] Y1: 0.3333 0.6667 0.2420 point group type: 3 special position operator: 1/3,2/3,z Si1: 0.5087 0.0819 0.2130 point group type: 1 special position operator: x,y,z Al1: 0.5087 0.0819 0.2130 point group type: 1 special position operator: x,y,z Si2: 0.1706 0.2533 0.0020 point group type: 1 special position operator: x,y,z Al2: 0.1706 0.2533 0.0020 point group type: 1 special position operator: x,y,z N1: 0.0000 0.0000 0.0000 point group type: 3 special position operator: 0,0,z O1: 0.0000 0.0000 0.0000 point group type: 3 special position operator: 0,0,z N2: 0.3333 0.6667 0.6530 point group type: 3 special position operator: 1/3,2/3,z O2: 0.3333 0.6667 0.6530 point group type: 3 special position operator: 1/3,2/3,z N3: 0.3458 -0.0472 -0.0050 point group type: 1 special position operator: x,y,z O3: 0.3458 -0.0472 -0.0050 point group type: 1 special position operator: x,y,z N4: 0.3219 0.3180 0.2460 point group type: 1 special position operator: x,y,z O4: 0.3219 0.3180 0.2460 point group type: 1 special position operator: x,y,z Other cif files give other missing gaussians: http://www.crystallography.net/cif/1/1000145.cif: > RuntimeError: gaussian not defined for scattering_type "V4+". http://www.crystallography.net/cif/1/1000181.cif: > RuntimeError: gaussian not defined for scattering_type "H1+". http://www.crystallography.net/cif/1/1000353.cif: > RuntimeError: gaussian not defined for scattering_type "H1+". I'm not sure if this is a problem related to the notation used in those cif files or if cctbx is missing some data here that should be added to it. With regards, Dipl. Pyhs. Jan M. Simons Institute of Crystallography RWTH Aachen University

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State of python3 support?
by Jan Marten Simons 15 Dec '10

15 Dec '10

Hi, as I've noticed from the changelogs cctbx is closely following python 2.x releases. Now I wonder if there are plans to move over to python3 soon? If I got it right, python 2.6 and 2.7 already offer most of python3 features and syntax as optional modules, so that the code can be prepared in advance (like converting print into print()-functions etc. [1] has some ideas on why and how to do a port. So I'm interested in your thoughts about python3 and cctbx. [1] http://peadrop.com/blog/2009/04/05/porting-your-code-to-python-3/ With regards, Jan M. Simons Institute of Crystallography RWTH Aachen

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How to load a structure from a .cif file?
by Jan Marten Simons 14 Dec '10

14 Dec '10

Hi, I've just started to work up some code for my phd. I've found cctbx to be quite a nice code base for my goals. So far I've seen that there is quite a large ammount of functions implemented, but in my opinion documentation on how to use them is either hidden or not in very verbose state. So from looking at the source I'm pretty confident that cctbx can load a crystalstructure from a .cif file (like those obtained from COD, http://www.crystallography.net/). But so far I've not been able to figure out how to do this. My experiments included: from iotbx import crystal_symmetry_from_any as sym_from_any from iotbx import file_reader file_name = "./xtal_data/9008806.cif" structure = file_reader.any_file(file_name) #gives an object, but not a structure # or structure = sym_from_any.extract_from(file_name) # returns none print(str(structure)) structure.show_summary().show_scatterers() Could you give me a hint into the right direction, please? With regards, Jan Simons

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Re: [cctbxbb] Help : CCTBX working
by Swapnil U Shinde 24 Nov '10

24 Nov '10

Hello I have installed CCTBX correctly and both tests run fine.Though when I try to import cctbx it throwing me error as 'no module named cctbx' e.g from cctbx import xray ImportError: No module named cctbx Does it mean python is not properly linked with cctbx.Please help me on this. Additional info: Python 2.6.6 Windows 7 OS Please let me know how to resolve this issue. Thanks in advance.. Thanks & Regards Swapnil U. Shinde ----- Original Message ----- From: Swapnil U Shinde <sshinde2(a)gmu.edu> Date: Tuesday, November 23, 2010 2:51 pm Subject: Help : CCTBX working > Hello > I am using EPD for python,numpy,scipy and cctbx on windows 7 > machine.(I compiled cctbx from windows studio 2010). Test results > for all are attached herewith. > In my code cctbx is accessed as - > ######### > cmmd2 = "cctbx.python \"" > cmddir = FIXDIR(os.getcwd()) > print "os.getcwd" > print os.getcwd() > print "****MML****: GetUnitCell_2.py" > cmmd2 = cmmd2 + cmddir + "GetUnitCell_2.py\"" > print "cmmd2" > print cmmd2 > #-------------------------------------- > # Execute GetUnitCell.py > #-------------------------------------- > bufsize = 1 > try: > print "*** Executing cctbx" > p2 = Popen(cmmd2, shell=True, bufsize=bufsize, stdin=PIPE, > stdout=PIPE, stderr=PIPE) > output2 = p2.communicate(input = allout) > ############# > cmmd2 is showing correct path of module GetUnitCell_2.py. However > output2 is coming empty which shows cctbx is not being accessed > properly. I am not sure whether it is because of faulty > installation or bug in code. > > Please advise how to proceed on this issue.I am stuck on it for > long time. > Thanks in advance!!! > > Thanks & Regards > Swapnil U. Shinde >

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Help : CCTBX working
by Swapnil U Shinde 23 Nov '10

23 Nov '10

Hello I am using EPD for python,numpy,scipy and cctbx on windows 7 machine.(I compiled cctbx from windows studio 2010). Test results for all are attached herewith. In my code cctbx is accessed as - ######### cmmd2 = "cctbx.python \"" cmddir = FIXDIR(os.getcwd()) print "os.getcwd" print os.getcwd() print "****MML****: GetUnitCell_2.py" cmmd2 = cmmd2 + cmddir + "GetUnitCell_2.py\"" print "cmmd2" print cmmd2 #-------------------------------------- # Execute GetUnitCell.py #-------------------------------------- bufsize = 1 try: print "*** Executing cctbx" p2 = Popen(cmmd2, shell=True, bufsize=bufsize, stdin=PIPE, stdout=PIPE, stderr=PIPE) output2 = p2.communicate(input = allout) ############# cmmd2 is showing correct path of module GetUnitCell_2.py. However output2 is coming empty which shows cctbx is not being accessed properly. I am not sure whether it is because of faulty installation or bug in code. Please advise how to proceed on this issue.I am stuck on it for long time. Thanks in advance!!! Thanks & Regards Swapnil U. Shinde

1 0

Help: cctbx installation and working
by Swapnil U Shinde 22 Nov '10

22 Nov '10

Hello I am new to cctbx user world and facing problem with cctbx working. I am having working python code with 3 libraries- Scipy Numpy cctbx I am using Enthought EPD which has python 2.6, scipy and numpy. http://www.enthought.com/products/epd.php All these things are working fine and then I installed cctbx from http://cctbx.sourceforge.net/current_cvs/installation.html#manually-buildin… (from Windows 2000 and higher) cctbx test cases are also running fine as there are no traceback calls.(test outputs are attached) However when I am running my python code it is giving error at cctbx interface. print "*** Executing cctbx" p2 = Popen(cmmd2, shell=True, bufsize=bufsize, stdin=PIPE, stdout=PIPE, stderr=PIPE) output2 = p2.communicate(input = allout) Here input (allout) is not empty but still output2 is coming empty which causes problems in next processing. It would be really great if you can tell me what problem is exactly and resolution on it. Please help me out in solving this issue.Let me know if you need more details. Hoping for your positive response!! Thanks in advance!!! -Swapnil U. Shinde

2 2

differential evolution
by Nikolay Mladenov 16 Nov '10

16 Nov '10

Hello all, Having nothing to do with crystallography, I downloaded cctbx only to use the python implementation of the differential evaluation. I am not knowledgeable about the details of the algorithm so I have to ask this question: Is it normal to have population members with coordinates outside of the specified limits? Thanks and regards, Nikolay Mladenov

2 4

Reducing coordinates to asymmetric unit
by Graeme.Winter＠Diamond.ac.uk 11 Feb '10

11 Feb '10

Hi Folks, Does anyone have a handy bit of CCTBX Python code which will take a spacegroup and unit cell, and a list of coordinates, and return the list of coordinates reduced to the asymmetric unit? I tried the "dumb" approach of: use unit cell and sites -> fractional sites for site in fractional sites: for smx in sg.smx() for ltr in sg.ltr() apply smx, ltr is in asu? return and it did not always return an answer, so there's clearly somthing I don't understand. Fractional coordinates are all in [0,1). I'm sure someone must have done this! Thanks in advance, Graeme Graeme Winter Software and MX Support 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 3

Bundled boost and scons
by Justin 04 Nov '09

04 Nov '09

Hi all, Is there a possibility to suppress the usage of bundled scons and boost and use the ones installed on the system? This has two reasons: first, I always like to not use bundled things if they are not heavily modified versions. Second,and that is more important in the moment. The bundled boost which I think is 1.39 has problems with >=python-2.6.3 [1]. So I'd like to use the installed boost-1.40 where the problem is already fixed by boost upstreams. Thanks justin [1] AttributeError: 'Boost.Python.StaticProperty' object attribute '__doc__' is read-only http://bugs.python.org/issue7183

2 1

using cctbx and sgtbx module
by hari jayaram 02 Nov '09

02 Nov '09

Hi I am trying to use a Python plugin SuperSymExample which has cctbx modules sgtbx and uctbx as dependencies. I wanted to build these modules for my system python 2.5.2 on ubuntu hardy heron 8.04 64 bit linux. I downloaded the selfx file for the cctbx alone ( without Python) and then had the build complete fully. I used the setpaths utility and then modifies m,y PYTHONPATH. Now after I add the appropriate directories to my PYTHONPATH , if I import sgtbx and uctbx in a python interactive session I get an error ( see below) My PYTHONPATH has: export PYTHONPATH="$PYTHONPATH:/rawdata12/cctbx_standalone/cctbx_sources:/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx" The error I get when I say from cctbx import sgtbx , uctbx: ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject What can I do to avoid the error and use the Plugin correctly. Thanks Hari Detailed error message: hari@charlie:/rawdata12/cctbx_auto/cctbx_build/lib$ python Python 2.5.2 (r252:60911, Jul 22 2009, 15:33:10) [GCC 4.2.4 (Ubuntu 4.2.4-1ubuntu3)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from cctbx import sgtbx,uctbx Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/sgtbx/__init__.py", line 2, in <module> from cctbx import uctbx File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/uctbx/__init__.py", line 1, in <module> from cctbx.array_family import flex File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/array_family/flex.py", line 1, in <module> import scitbx.array_family.flex File "/rawdata12/cctbx_standalone/cctbx_sources/scitbx/array_family/flex.py", line 1, in <module> import boost.optional File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in <module> import boost.python File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in <module> ext = import_ext("boost_python_meta_ext") File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject sys.path: /usr/lib/python2.5/site-packages /rawdata12/wx-widgets-read-only/wxPython /home/hari/ccp4-6.0.99e/share/python /rawdata12/cctbx_auto/cctbx_build/lib /home/hari /rawdata12/cctbx_standalone/cctbx_sources /rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx /usr/lib/python25.zip /usr/lib/python2.5 /usr/lib/python2.5/plat-linux2 /usr/lib/python2.5/lib-tk /usr/lib/python2.5/lib-dynload /usr/local/lib/python2.5/site-packages /usr/lib/python2.5/site-packages /usr/lib/python2.5/site-packages/Numeric /usr/lib/python2.5/site-packages/PIL /home/hari/djtrunk /usr/lib/python2.5/site-packages/kodos /usr/lib/python2.5/site-packages/gst-0.10 /var/lib/python-support/python2.5 /usr/lib/python2.5/site-packages/gtk-2.0 /var/lib/python-support/python2.5/gtk-2.0 /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode

2 2

Strange segementation fault
by Armin Moser 28 Jul '09

28 Jul '09

Dear cctbx-developers, I recently started to use the cctbx. Some days before i may have found a bug. Description: When I import from the cctbx and perform a division through zero (with array objects from numpy) something segfaults. I've appended a script that demonstrates this behaviour. Maybe it's just a problem with my specific system (I did not observe this behaviour on windows). I've compiled the cctbx from the unix sources with the build tag 2008_09_13_0905 on a debian testing system: Python 2.5.4, gcc 4.3.3, libboost.python1.37.0 Do you need information on other libraries too? Can anybody reproduce this or has an idea what could be wrong? Maybe someone can give me a hint how I could try to debug this? Thanks Armin -----------------8<--------------------8<------------ import numpy as np a = np.array([[1,2,3],[4,5,6]]) b = np.zeros(a.shape) b[[0,0,1],[1,2,0]] = 1 c = a/b print 'before import x/0 is not a problem' print c import cctbx from cctbx import xray, crystal, miller, sgtbx, uctbx from cctbx_array_family_flex_ext import miller_index import scitbx_array_family_flex_ext from iotbx.shelx import from_ins lo = b!= 0 c = np.ones(a.shape)*np.inf c_div = a[lo]/b[lo] c[lo] = c_div print 'after import workaround' print c print 'after import x/0 ==> segfault' print a/b

3 3

spec file for cctbx rpm (on F10)
by Cameron Mura 28 Jul '09

28 Jul '09

Hi all, In case it's of interest, I've attached a spec file that works for building a cctbx RPM on Fedora 10 (nothing really F10-specific, so may work on other distros/releases too). Please note that it works by playing the dangerous (and extremely ugly) game of moving the RPM build into the system-wide tree, so it builds "in situ" in /usr/local/cctbx instead of in the RPM default locale (/my/rpm/BUILDROOT/usr/local/cctbx). On the same note, the patch which is referenced in the spec file ('cctbx_bundle_StrucBio.patch') is just a small snippet that edits the head of 'cctbx_install_script.csh' to explicitly control the build path (i.e., override $cwd by explicitly setting something like 'set install_root="/usr/local/cctbx/2009_02_15_2320"', or wherever you'd like cctbx to live...). Probably a much cleaner procedure would be to use the libtbx/configure.py approach in a post-processing step; let me know if anyone pkg's an RPM that way. :-) Enjoy, Cam -- ------------------------------------------------------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cmura(a)virginia.edu Web: http://muralab.org Tel: 434.924.7824 Fax: 434.924.3710 ------------------------------------------------------- #------------------------------------------------------------------------------- # Cameron Mura <cmura(a)virginia.edu>; 27jul09; #------------------------------------------------------------------------------- %define _buildroot /usr/local/cctbx/2009_02_15_2320 %define debug_package %{nil} #%define _builddir /usr/local/cctbx/2009_02_15_2320 Name: cctbx Version: 2009_02_15_2320 Release: 1 Summary: Computational Crystallography Toolbox License: Open Source (BSD-like) Group: Applications/Engineering URL: http://cctbx.sourceforge.net Source0: %{name}_bundle_%{version}.tar.gz Source1: ccp4_mon_lib.tar.gz Packager: Cameron Mura <cmura(a)virginia.edu> Patch0: cctbx_bundle_StrucBio.patch #BuildRoot: /var/tmp/%{name}-buildroot BuildRoot: /usr/local/cctbx/2009_02_15_2320 %description The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system. The goal of the PHENIX project is to advance automation of macromolecular structure determination. PHENIX depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications. The cctbx is designed with an open and flexible architecture to promote extendability and easy incorporation into other software environments. The package is organized as a set of ISO C++ classes with Python bindings. This organization combines the computational efficiency of a strongly typed compiled language with the convenience and flexibility of a dynamically typed scripting language in a strikingly uniform and very maintainable way. Note that CCTBX is developed under an open source (BSD-like) license; for addition information, see http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/cctbx/LICENSE_2_0.txt. %prep # Require weird gymnastics to relocate cctbx outside the RPM build tree... #export MYCCTBXHOME="/usr/local/cctbx/2009_02_15_2320" #if [ ! -d $MYCCTBXHOME ]; then # mkdir -p $MYCCTBXHOME #fi %setup -a 0 -D -c /usr/local/cctbx/2009_02_15_2320 -n . cp %{_topdir}/SOURCES/ccp4_mon_lib.tar.gz /usr/local/cctbx/2009_02_15_2320/. #%setup -a 1 -D -T -c /usr/local/cctbx/2009_02_15_2320 -n . %patch0 -p1 %build /usr/local/cctbx/2009_02_15_2320/cctbx_install_script.csh /usr/bin/python 8 . "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.sh" libtbx.unpack_in_sources ccp4_mon_lib.tar.gz %install mkdir -p $RPM_BUILD_ROOT/usr/local/cctbx/2009_02_15_2320 mv /usr/local/cctbx/2009_02_15_2320/* $RPM_BUILD_ROOT/usr/local/cctbx/2009_02_15_2320/. mkdir -p $RPM_BUILD_ROOT/etc/profile.d echo '. "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.sh"' > $RPM_BUILD_ROOT/etc/profile.d/cctbx.sh echo 'source "/usr/local/cctbx/2009_02_15_2320/cctbx_build/setpaths.csh"' > $RPM_BUILD_ROOT/etc/profile.d/cctbx.csh #chmod 755 $RPM_BUILD_ROOT/etc/profile.d/cctbx.sh #chmod 755 $RPM_BUILD_ROOT/etc/profile.d/cctbx.csh #[ $RPM_BUILD_ROOT != "/" ] && rm -rf $RPM_BUILD_ROOT #install -m 755 src/rasmol_32BIT $RPM_BUILD_ROOT/usr/local/rasmol #install -m 755 src/rasmol_XFORMS_32BIT $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 doc/rasmol.hlp $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 INSTALL* $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 README* $RPM_BUILD_ROOT/usr/local/rasmol #install -m 644 TODO* $RPM_BUILD_ROOT/usr/local/rasmol #cp -R working/cctbx_sources $RPM_BUILD_ROOT/usr/local/cctbx/%{version} #cp -R working/cctbx_build $RPM_BUILD_ROOT/usr/local/cctbx/%{version} %clean [ $RPM_BUILD_ROOT != "/" ] && rm -rf $RPM_BUILD_ROOT %post #ln -fs /usr/local/rasmol/rasmol_32BIT /usr/local/bin/rasmol %preun #%{__rm} -f /usr/local/bin/rasmol %files %defattr(-,root,root) #%doc ChangeLog.txt ChangeLog.html INSTALL* NOTICE README* /usr/local/cctbx/2009_02_15_2320 /etc/profile.d/%{name}.sh /etc/profile.d/%{name}.csh %changelog * Sun Jul 26 2009 Cameron Mura <cmura(a)virginia.edu) 2009_02_15_2320-1 - Initial RPM build on Fedora 10...

1 1

draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?
by Cameron Mura 06 Jul '09

06 Jul '09

Hi all, Apologies for the message to both mailing lists, but perhaps someone on either cctbxbb or pymol-users has had some recent experience with this... The subject line more-or-less says it all: I'm wondering if anyone has recently used Rob Campbell's draw_symops (or draw_symops_cctbx) Python modules with a relatively recent (within past year) version of the cctbx (particularly the Boost C++ parts) ? I succeeded in doing this a few years ago to generate images such as the ones near the top of http://muralab.org/~cmura/PyMOL/Sandbox/, but I can't get it to work on my present system (64-bit Fedora 10; Python 2.5.2 with Python 2.6 coexisting). Below is what happens when I... 1) Initiate a new PyMOL session (using a PyMOL v1.1 that I built in-place from source, so should be compatible with local python, system libs, etc) 2) load PDB files (tried with a few diff't files; verified that they contain proper CRYST specifications) 3) do the usual 'run draw_symops_cctbx.py' 4) call draw_symops() -- either implicitly, or by explicit specification of the u.c. params (i.e., using something like "draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)") ...which crashes the pymol session and yields the following trace: > PyMOL>draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1) > libc backtrace (48 frames, most recent call last): > /usr/bin/python [0x400649] > /lib64/libc.so.6(__libc_start_main+0xe6) [0x344081e576] > /usr/lib64/libpython2.5.so.1.0(Py_Main+0xb11) [0x34584e7ef1] > *<snip> > ... > ... > </snip>* > /usr/lib64/libpython2.5.so.1.0(PyObject_Call+0x13) [0x345843d493] > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so > [0x7ff19691db16] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x9f) > [0x7ff19692a2ef] > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so > [0x7ff196920b08] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::objects::function::call(_object*, > _object*) const+0x125) [0x7ff196920635] > > /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so(boost::python::detail::caller_arity<2u>::impl<cctbx::sgtbx::rt_mx > (*)(cctbx::sgtbx::space_group const&, unsigned long), > boost::python::default_call_policies, > boost::mpl::vector3<cctbx::sgtbx::rt_mx, cctbx::sgtbx::space_group > const&, unsigned long> >::operator()(_object*, _object*)+0x12a) > [0x7ff18f820a3a] > /root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so > [0x7ff18f8034cc] > > /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::throw_error_already_set()+0xe) > [0x7ff196929dde] > /usr/lib64/libstdc++.so.6(__cxa_allocate_exception+0x2f) [0x3444cc2cdf] > /lib64/libc.so.6 [0x3440832f90] > Segmentation fault (libc call stack above) > This crash may be due to a problem in any imported > Python module, including modules which are not part > of the cctbx project. To disable the traps leading > to this message, define these environment variables > (e.g. assign the value 1): > BOOST_ADAPTBX_FPE_DEFAULT > BOOST_ADAPTBX_SIGNALS_DEFAULT > This will NOT solve the problem, just mask it, but > may allow you to proceed in case it is not critical. > PyMOL: abrupt program termination. I tried the recommendation of setting the BOOST_ADAPTBX* env vars, but this doesn't remedy the problem. Also, I tried accomplishing this with many combinations of workflows: 1) old cctbx (e.g., 2005_04_29_1615), latest stable release of cctbx (2009_02_15_2320), bleeding-edge cctbx (2009_07_04_0143) 2) pre-built cctbx binaries versus building myself from src (for each of the above), insuring, again, optimal match between local system libs... 3) cctbx alone, cctbx in the context of Phenix, cctbx +/- its own bundled Python (2.5 and 2.6) Also, I tried this with different combinations of Rob's scripts -- e.g., the 'symop_axes.dat'-dependent "draw_symops.py", versus the 'all_axes_new.py'-dependent "draw_symops_cctbx.py". Interestingly, I found that get_all_axes() from 'all_axes_new.py' works fine for different PDB files. Investigating the above draw_symops stacktrace led me to this post from Ralf Grosse-Kunstleve to python-dev: http://mail.python.org/pipermail/python-dev/2008-September/082639.html It looks like exactly the same problem that's causing the pymol/draw_symops scripts to choke. Also, I can verify that issuing commands such as in Ralf's post (boost_adaptbx.segmentation_fault, boost_adaptbx.divide_by_zero) result in the same segfaults and errors as in his post, so... I believe this is the crux of it. Before delving into Boost codebase, cctbx's exception-handling in C++/Python Boost, etc., I'm wondering if anyone else has seen anything like this...? or has advice on how best to proceed? Any tips or suggestions would be most greatly appreciated. Thanks, Cam -- ------------------------------------------------------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cmura(a)virginia.edu Web: http://muralab.org Tel: 434.924.7824 Fax: 434.924.3710 -------------------------------------------------------

2 3

Reindexing matrix -> transform orientation matrix
by Winter, G (Graeme) 05 May '09

05 May '09

Hi Folks, I'm just trying to figure out how to do the following, given a triclinic orientation matrix (real or reciprocal space, differ by .inverse() -> triclinic unit cell) (like iotbx.lattice_symmetry) stuff -> set of unit cell, Bravais lattice options with reindex operations apply reindex operation to orientation matrix -> new basis a, b, c The former I have historically done using iotbx.lattice_symmetry but given the move from python to cctbx.python, it seems wasteful. I looked at the source code but got a little confused. The latter seems to be more problematic - even reconstructing the change of basis from a known reindexing operation I don't seem to be able to get the right answer :o( Has anyone done anything like this with the CCTBX tools? The context is autoindexing with XDS using a full sweep's worth of images, then inspecting the indexes in SPOT.XDS based on the contents of XPARM.XDS. Thanks, Graeme Graeme Winter Software and MX Support 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 2

cctbx geometry modules?
by Artem Evdokimov 31 Dec '08

31 Dec '08

Hi, Sorry to ask a possibly obvious question - but I am very new to cctbx and an absolute novice of python :-) Apologies in advance. Quesiton 1 - is there a web site or some other form of a source for a complete cctbx documentation, most importantly with simple working examples? I've been using some of the examples published in the newsletters but they're scattered here and there. Maybe there is a cctbx wiki somewhere? Question 2 - is there anything inside cctbx that can compute elements of protein geometry - such as dihedral angles, planes, etc. (given selections of atoms)? Thanks in advance! Happy New Year! Cheers, Artem

2 1

Re: [cctbxbb] structure factor interpolation
by celine Besnard 19 Nov '08

19 Nov '08

Hi Ralf and Jon, Thanks a lot for your help. I will try to follow your advices. Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

1 0

structure factor interpolation
by celine Besnard 07 Nov '08

07 Nov '08

Hi, I am looking for a function that would allow me to interpolate the structure factors values in between the reciprocal lattice points (h,k,l not integer) so that I can get the reciprocal map not of the whole crystal but of "only one" unit-cell. Is there a simple way to do that in the cctbx ? Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

3 3

postdoc position in LBNL
by Peter Zwart 21 Oct '08

21 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

Re: [cctbxbb] interpreting auto generated python interface documentation
by Ralf W. Grosse-Kunstleve 28 Aug '08

28 Aug '08

> Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html, > the documentation gives me a "cache" class __init__ method that says > > __init__(self, root, wildcard_escape_char=r'\') > > How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments. It is a iotbx.pdb.hierarchy.root instance in this case, mostly referred to as "pdb_hierarchy" or just "hierarchy". Yes, for some things you have to go into the code. The best approach is to insert print statements to see what the objects are, then run the associated tests (e.g. iotbx/pdb/tst_*.py). > In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html > return an error page. Thanks for pointing this out. I'll look into this next week, when I'm back home. > I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Don't hesitate to ask. You may have many questions at first, but then they'll become fewer and far in between. I'll respond more promptly after the conference trip. Ralf

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Re: [cctbxbb] input_atom_labels_list() not available in Python?
by Ralf W. Grosse-Kunstleve 27 Aug '08

27 Aug '08

Hi Hari, > input_atom_labels_list() > This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses > this function > However I dont see that in the python interface with the current version? Is that true or am I using a different build > that does not make this available in python That method is gone, indeed, ever since about April/May this year. Look for "atoms_with_labels": cd cctbx_sources libtbx.find_files -g atoms_with_labels -f Ralf P.S.: Have to run now... will look at your other email later.

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input_atom_labels_list() not available in Python?
by hari jayaram 26 Aug '08

26 Aug '08

Thanks Nathaniel.. I too was using the approach of looking at the phenix scripts to figure things out. But I was hoping that there was a "google hidden" source of documentation for the python interfaces that I was not aware of. For the present moment the c++ documentation is much more useful .After I sent the email out , I did notice the section in the manual which says.. "Most documented C++ interfaces are also available at the Python layer. Unfortunately the documentation tools available are not capable of merging the documentations. Therefore Python users need to also consult the C++ documention." On an unrelated note The Nov 2006 newsletter and the c++ and python documentation lists a function in the class iotbx.pdb.input called input_atom_labels_list() This function seems to be available from both c++ and python. The Nov 2006 letter has a python example that uses this function However I dont see that in the python interface with the current version? Is that true or am I using a different build that does not make this available in python Just curious Hari On Tue, Aug 26, 2008 at 12:50 PM, Nathaniel Echols < nathaniel.echols(a)gmail.com> wrote: > Having spent the last few months trying to learn the python side of cctbx > for my own work, I recommend looking at some of the actual programs that > call these functions (e.g. the various phenix scripts, or testing scripts) > for clues on how to use them. In particular, > iotbx/pdb/tst_atom_selection.py has examples of selection caches. (I'm not > sure how exactly the "cache" class fits in, since it isn't invoked directly > in that script, but hopefully the test script has some approximation of what > you're trying to do.) I haven't found it necessary to look at the C++ code > - boost.python obscures many details anyway, and it's usually pretty obvious > to me what's going on in the python sources based on the > variable/class/function names. > The various CCP4 newsletter articles may have some useful suggestions, but > I haven't looked at these in much detail yet. > > On Tue, Aug 26, 2008 at 9:18 AM, hari jayaram <harijay(a)gmail.com> wrote: > >> Hi , >> I am a few days into learning to use the cctbx libraries. My interests >> are mostly to be able to write scripts that plot various statistics from mtz >> files and use things like iotbx.pdb to manipulate coordinate files. While I >> have managed to write a few scripts and have read the very descriptive >> examples in the newsletters and the few routines inside of phenix. I have >> a problem with getting much out of the python interface documentation at the >> sourceforge site. >> >> Say , for a particular class say >> http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html >> , >> the documentation gives me a "cache" class __init__ method that says >> >> __init__(self, root, wildcard_escape_char=r'\') >> >> How do I find out what "root" is in this example. Should I be looking at >> the c++ code to find out the "types" of these arguments. >> >> In addition a few of the auto-generated documentation pages such as >> http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html >> return an error page. >> >> I just want to know a good way of understanding the varrious interfaces >> when writing code using cctbx in Python >> Thanks in advance >> hari >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/cctbxbb >> >> > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/cctbxbb > >

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interpreting auto generated python interface documentation
by hari jayaram 26 Aug '08

26 Aug '08

Hi , I am a few days into learning to use the cctbx libraries. My interests are mostly to be able to write scripts that plot various statistics from mtz files and use things like iotbx.pdb to manipulate coordinate files. While I have managed to write a few scripts and have read the very descriptive examples in the newsletters and the few routines inside of phenix.I have a problem with getting much out of the python interface documentation at the sourceforge site. Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html, the documentation gives me a "cache" class __init__ method that says __init__(self, root, wildcard_escape_char=r'\') How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments. In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html return an error page. I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python Thanks in advance hari

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Re: [cctbxbb] getting resolution for any "h" "k" "l" and cctbx
by Ralf W. Grosse-Kunstleve 05 Aug '08

05 Aug '08

Hi Hari, > 1) I was wondering if someone can point me to routines available from > cctbx modules that can give me the "resolution" for a given index "h" > "k" "l". in any space group To get the resolution for a given hkl, you just need the unit cell: from cctbx import uctbx uc = uctbx.unit_cell((11,12,13,93,98,103)) hkl = (2,3,4) print uc.d(miller_index=hkl) print uc.stol(miller_index=hkl) wavelength = 1.3 print uc.two_theta(miller_index=hkl, wavelength=wavelength) Save as "resolution_hkl.py" and run with: cctbx.python resolution_hkl.py The .d(), .stol(), .two_theta() methods are documented here: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1uni… > 2) In addition , if someone can point me in the direction of a well > illustrated depiction of the derivation of the reciprocal lattice > for the triclinic case , that will be very much appreciated bonus . I'm not sure which textbook to recommend. I liked the old Buerger books a lot, but I don't remember how he introduces the reciprocal lattice. Ralf

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getting resolution for any "h" "k" "l" and cctbx
by hari jayaram 05 Aug '08

05 Aug '08

Hi , I have been programming in python for a little bit, I am new to cctbx . My crystallography knowledge is as good as solving a few structures gives you. I have a few questions. 1) I was wondering if someone can point me to routines available from cctbx modules that can give me the "resolution" for a given index "h" "k" "l". in any space group 2) In addition , if someone can point me in the direction of a well illustrated depiction of the derivation of the reciprocal lattice for the triclinic case , that will be very much appreciated bonus . Thank you in advance Hari

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Re: [cctbxbb] (no subject)
by Ralf W. Grosse-Kunstleve 26 May '08

26 May '08

Hi Xie, > Are cctbx and phenix compatible with a 64 bit operating system? Yes. > I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Please try the source bundle: cctbx_python_252_bundle.selfx http://cci.lbl.gov/cctbx_build/ Let me know if there are any problems. Ralf

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(no subject)
by Xie Jiabao 26 May '08

26 May '08

Hi, Are cctbx and phenix compatible with a 64 bit operating system? I have Ubuntu 8.04 (64 bit) installed on an Intel Core2 duo system. Thanks, Xie

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Re: [cctbxbb] problem in "space_group_type"
by Ralf W. Grosse-Kunstleve 16 Apr '08

16 Apr '08

Hi Koen, > The error only occurs when running in Debug mode. In Release mode, > everything works fine, suggesting a memory initialization problem. This is a known feature of Windows: libraries compiled in release and debug mode are not binary compatible. Under Linux I check with valgrind all the time, therefore it is almost certain that the Windows debug/release mix is the only problem. > I'm unable to debug the problem myself or get more details, as I can't > get the library to compile with debugging information in it (Is there an > easy way to do this with the Scons build system? I haven't used Scons > before.) The *one* script to change is libtbx/SConscript Currently, in the if (sys.platform == "win32"): ... if (env_etc.compiler == "win32_cl"): branch you'll find: if (libtbx.env.build_options.debug_symbols): raise RuntimeError("Debug build not supported.") This is the place to start. On Unix platforms it simply works like this: if (libtbx.env.build_options.debug_symbols): opts.insert(0, "-g") I forgot the details of why it is more complicated under Windows. I vaguely recall that there were issues linking with the correct runtime libraries, in particular linking with the correct Python runtime. Idea: replace the RuntimeError above with opts.insert(0, "???") and initialize a new build directory with libtbx\configure.py --build-boost-python-extensions=False --build=debug Since you are not building Python extensions, the Python runtime library problem goes away. Ralf

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problem in "space_group_type"
by Koen De Keyser 16 Apr '08

16 Apr '08

Hi, I'm currently in the process of writing some texture analysis/visualization software (XRD pole figures, EBSD) and would like to use cctbx as a basis for the crystallography calculations, as I don't want to reinvent the wheel. Development is in C++ on Windows, and trying one of the examples from the code, I end up being able to crash the program, when running: space_group_type sg_type("C 2"); This occurs using the latest release and still happens in the (unreleased) code from 13th of April, both times, I compiled the library from source, using Visual Studio 2005 and 2008. It looks to me that the problem is situated in the Hall symbol part of the space group (those structures are indicated as bad_ptr in the debugger, when crashing) The error only occurs when running in Debug mode. In Release mode, everything works fine, suggesting a memory initialization problem. I'm unable to debug the problem myself or get more details, as I can't get the library to compile with debugging information in it (Is there an easy way to do this with the Scons build system? I haven't used Scons before.) thanks, Koen De Keyser -- ir. Koen De Keyser Solid State Sciences Ghent University Krijgslaan 281, S1 9000 Gent, Belgium Tel: +32 9 264 43 54 Fax: +32 9 264 49 96 Koen.DeKeyser(a)UGent.be

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Centos rpm
by Pascal 27 Mar '08

27 Mar '08

Hi, I didn't see any rpms for centos. Do you mind if I'll make one ? Is the spec file for fedora available somewhere ? Regards, Pascal -- Pascal Parois Glasgow university http://centos.parois.net

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Re: [cctbxbb] solvent mask
by Ralf W. Grosse-Kunstleve 18 Oct '07

18 Oct '07

Hi Celine, > Thank you for all those explanation. In fact the problem for me is not > the mean of the recalculated map obtained but the range of it, which is > no longer one. Did you consider using the raw mask with the ones and zeros directly? That's the .data attribute of the bulk_solvent object. It is an integer array, but you can convert it with .data.as_double(). See also the .mask_as_xplor_map() method. The only thing the FFT back and forth does is to introduce the Ewald-sphere truncation, which leads to a smoothing of the original mask. If you want that, a quick-and-dirty approach is to copy the .structure_factors() method, rename it, then replace miller_set.unit_cell().volume() with 1.0 in the computation of scale. I think you still need to divide by the number of grid points. Use the .fft_map() of the structure factors object (miller.array) returned by your modified method to get back a map with truncation effects, but on the same scale is the original mask. > To be more clear, what I am trying to do is to "calculate" data at > different solvent contrasts from a pdb file. So I have a series of > solvent electron densities and I would like to use the complex formula F > = Fprotein in vacuum + solvent density*Fmask where Fmask are the > structure factors from an indicator function that is 1 in the solvent > region and 0 in the protein region (= my cctbx mask). That sounds exactly like what's done by the f_model class, which will refine the "solvent density" for you. I think you can also specify a value. See mmtbx/mmtbx/examples/f_model_manager.py and the Computing Commission Newsletter No. 5 (http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf). The code in the newsletter article is out of date, but the math is still accurate and examples/f_model_manager.py is the updated code. Fcalc in the newsletter formula (page 10 of the .pdf document) is your "Fprotein in vacuum". ksol is your "solvent density". You can set Uaniso and Bsol to 0 if you want. Ralf

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Re: [cctbxbb] solvent mask
by Ralf W. Grosse-Kunstleve 15 Oct '07

15 Oct '07

Hi Celine, > I have a question about solvent mask in cctbx. I generated a mask using > the mask manager. Then I am calculating the structure factors from the > mask (using mask_manager.structure_factors() ). If I am trying to redo a > map from the calculated structure factors (outside the cctbx and I hope > without any scaling), I get a map with a mean density of zero, That's because the F000 is missing. Without the F000, the mean of an FFT map will always be exactly zero. -- This is a general feature of discrete Fourier transforms. > So I wonder what is exactly this > matrix.col(fft_manager.n_real()).product() doing? That's the number of grid points in the map. The FFT introduces this as a scale factor which we are taking out. -- Again, the number of grid point issue is a general feature of discrete Fourier transforms. > And how do I generate > structure factors for a mask without any scaling? I'm guessing the scaling is not the problem, but just the absence of F000, which you can get as map_of_coeff[0]. I think it will also work if you give an array of Miller indices including (0,0,0). We could add suppress_scaling to the signature of the .structure_factors() method, but the scale is rather arbitrary anyway, so I don't think this will be very useful. Ralf

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coordinates -> space group + matrices
by Kris Andersen 15 Oct '07

15 Oct '07

This is probably a simple (maybe stupid) question, but that never stopped me before: I want to give cctbx a set of primitive vectors and coordinates (cartesian or fractional), and have it return (1) the space group and (2) all the symmetry matrices. For example, given R = [4 0 0 % primitive vectors 0 4 0 0 0 4] x = [0.00 0.0 0.00 % fractional coordinates 0.51 0.51 0.51 0.50 0.50 0.00 0.00 0.50 0.50 0.50 0.00 0.50] I want cctbx to tell me this is space group #160 R3m, that there are 6 symmetry operations, and give me the corresponding matrices. This sounds easy, given everything cctbx can do, so it must be possible. Is there a simple example anywhere? Thanks. -- Kristopher E. Andersen http://www.physics.nau.edu/~andersen/ Northern Arizona University kris.andersen(a)nau.edu Department of Physics and Astronomy (928) 523-7202

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Re: [cctbxbb] coordinates -> space group + matrices
by Ralf W. Grosse-Kunstleve 18 Sep '07

18 Sep '07

Hi Kris, your questions isn't simple and the solution isn't straightforward. The functionality you are looking for isn't implemented in the cctbx. You are right in your assumption that most of what you need is already available, but there are missing pieces. Given a unit cell (your primitive vectors), the cctbx can give you the corresponding highest point-group symmetry (lattice symmetry) in a very robust way, but there is nothing to loop over the compatible space groups and to check if the symmetry operations are compatible with the coordinates. There are some programs out there which do this. I think Ton Spek's PLATON for example. The Superflip program (google) determines the symmetry from a P1 map. There is also J. Appl. Cryst. (2005). 38, 237-238 and J. Appl. Cryst. (1998). 31, 922-928. There may be more. I haven't followed the developments very closely. An idea that has been floating around in my mind for a long time is to use the fast translation function. Make a map given your coordinates, loop over all space group, use the fast translation function to find the origin. This is implemented in phenix.hyss. It should be relatively easy to adapt this implementation for your purpose. You'd get scores (correlation coefficients) instead of yes/no answers. This could be useful to uncover approximate symmetry, but I'm just guessing. If you want to try implementations yourself, I'd be happy to answer specific questions. Ralf ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Re: [cctbxbb] structure_factors_from_map
by Ralf W. Grosse-Kunstleve 09 Jul '07

09 Jul '07

Hi Philipp, The two FFTs introduce a scale factor equivalent to the number of grid points. Please try adding this code: x = abs(new_array).data() y = abs(very_new_array).data() lc = flex.linear_correlation(x, y) lc.show_summary() lr = flex.linear_regression(x, y) lr.show_summary() The correlation coefficient should be 1.0 exactly, and the linear-regression slope is the same as the "total number of grid points" shown in the output: total number of grid points: 345600 ... is_well_defined: True mean_x: 43.9292797741 mean_y: 15181959.0899 coefficient: 1.0 is_well_defined: True y_intercept: 5.1687812285e-07 slope: 345600.0 Ralf ____________________________________________________________________________________Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/

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Re: [cctbxbb] pdb output
by Ralf W. Grosse-Kunstleve 09 Jul '07

09 Jul '07

Hi Celine, There isn't something like a pdb.output object, but there are a few helper functions for writing certain records. E.g. see section 5.6 of this newsletter: http://cci.lbl.gov/publications/download/iucrcompcomm_nov2006.pdf Look for "def format_" in iotbx/iotbx/pdb/__init__.py. Ralf ----- Original Message ---- From: celine Besnard <celine.besnard(a)epfl.ch> To: cctbxbb(a)phenix-online.org Sent: Monday, July 9, 2007 9:02:05 AM Subject: [cctbxbb] pdb output Hello I have a structure object which I want to write a pdb file from. Is there any function that does the contrary of the pdb.input function in the iotbx? I have not been able to find one. Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/cctbxbb ____________________________________________________________________________________ Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091

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pdb output
by celine Besnard 09 Jul '07

09 Jul '07

Hello I have a structure object which I want to write a pdb file from. Is there any function that does the contrary of the pdb.input function in the iotbx? I have not been able to find one. Thanks Celine -- Dr. Céline Besnard EPFL - SB - IPMC - LCR2 CH-1015 Lausanne Suisse e-mail : Celine.Besnard(a)epfl.ch Tel : +41(0)21.693.05.41 Fax : +41(0)21.693.05.04 http://lcr.epfl.ch

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