- cctbxbb - phenix-online.org

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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