- cctbxbb - phenix-online.org

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 04 Jun '11

04 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 11 Feb '11

11 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 24 Dec '10

24 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 16 Dec '10

16 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 25 Nov '10

25 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 24 Nov '10

24 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

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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

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differential evolution
by Nikolay Mladenov 17 Nov '10

17 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

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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

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Bundled boost and scons
by Justin 05 Nov '09

05 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

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using cctbx and sgtbx module
by hari jayaram 03 Nov '09

03 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

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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

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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 08 Nov '08

08 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

1 0

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.

1 0

input_atom_labels_list() not available in Python?
by hari jayaram 27 Aug '08

27 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 > >

1 0

interpreting auto generated python interface documentation
by hari jayaram 27 Aug '08

27 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

2 1

Re: [cctbxbb] getting resolution for any "h" "k" "l" and cctbx
by Ralf W. Grosse-Kunstleve 06 Aug '08

06 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

1 0

getting resolution for any "h" "k" "l" and cctbx
by hari jayaram 06 Aug '08

06 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

1 0

Re: [cctbxbb] (no subject)
by Ralf W. Grosse-Kunstleve 27 May '08

27 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

1 0

(no subject)
by Xie Jiabao 27 May '08

27 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

1 0

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

1 0

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

1 0

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

1 0

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 16 Oct '07

16 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 19 Sep '07

19 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 10 Jul '07

10 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 10 Jul '07

10 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 10 Jul '07

10 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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structure_factors_from_map
by Philipp Heuser 09 Jul '07

09 Jul '07

Hi, thanks for the help with my asymmetric unit problem again. However I do have further questions further down my pipeline regarding the backwards fft from the map to structure factors: Am I right if I assume that fft_map = new_array.fft_map(resolution_factor=1/3., symmetry_flags=maptbx.use_space_group_symmetry) real_map = fft_map.real_map() very_new_array=new_array.structure_factors_from_map(map=real_map) #Output1 new_array.show_array() #Output2 very_new_array.show_array() Output1 and Output2 should be identical? They are not... Do I have to consider something, so that they are identical? Thanks and kind regards Philipp -- -------------------------------------------------- Dr Philipp Heuser Postdoctoral fellow EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 188 fax: +49 40 89902 149 mail: philipp.heuser(a)embl-hamburg.de web: www.philipp-heuser.de --------------------------------------------------

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 25 Jun '07

25 Jun '07

Hi Phillip, Could you give a brief overview of what you want to do? There are many ways of handling the contiguous asu information, but how much effort a particular approach is worth highly depends on the application. E.g. it is important to understand how important runtime performance is vs. memory use vs. developer time. Note that the contiguous asymmetric units are fully defined in the cctbx.sgtbx.direct_space_asu module (this is behind the asu gallery Peter pointed out). However, the full information for handling all conditions on the facets, edges and vertices is only available in Python. For processing maps this is likely to be too slow, unless you really don't care about runtime. In C++, the contiguous asymmetric units are only used as volumes: cctbx/crystal/direct_space_asu.h, classes float_cut_plane and float_asu, which duplicate some of the Python code. It is not a severe duplication since the facet/edge/vertex conditions are meaningless when working with floating-point numbers and can therefore be dropped. When dealing with grid points in maps you need those conditions somehow, either from some sort of reference table as we have in Python, or by looping over the symmetry operations. Handling the full conditions in C++ would be quite a bit of work, I think. It would be cool to have in general, but so far I didn't have an application important enough to justify the effort. Ralf ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 23 Jun '07

23 Jun '07

Hi Phillip, sorry, that was an oversight. Replace - real_map = fft_map.real_map() + real_map = fft_map.real_map_unpadded() and it should print identical values. > Is there any reason for the different sizes of the tag_array and the > real_map? real_map.last() and tag_array.last() show different results. That was exactly the problem. The real_map is padded because of FFT requirements. The tag_array is not. .real_map_unpadded() will make a copy. There will be another copy to restore the padding in .structure_factors_from_map() call. The two copies can be avoided in C++, but it is to cumbersome from Python. Ralf ____________________________________________________________________________________ Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/

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Re: [cctbxbb] Asymmetric Unit with cctbx
by Ralf W. Grosse-Kunstleve 20 Jun '07

20 Jun '07

Hi Philipp, You can find an expanded version of your script here: http://cci.lbl.gov/~rwgk/tmp/cctbx_examples/2007_06_17/ Use this command to generate a fake mtz file: iotbx.python random_f_calc.py P31 Then this command: iotbx.python mtz_to_map_and_back.py random_f_calcs.mtz FC1 FC2 This illustrates how to convert a manipulated map back to Fourier coefficients (via .structure_factors_from_map()) and write these out in MTZ format. In the example, the map manipulation is simply squaring the map. You can do anything else with the map from Python. For the FFT back to Fourier coefficients, you need a map over the unit cell. For maps, we don't have continuous asymmetric units (the map code pre-dates the ASU gallery). Instead, we have a "tag array" of integer values with the same gridding as the data map. An integer value less than 0 means "this grid point is unique under symmetry", values >= 0 are the 1D indices of the symmetry-related unique point. See the code near the end of mtz_to_map_and_back.py. It shows a loop over the grid points accessing both the tag_array and the real_map. This loop is slow, of course, since it is in Python. It should be fast enough for prototyping, but I'd expect the final version to be implemented in C++, unless your manipulation can be formulated with existing array algebra, e.g. the flex.pow2() in the example, which already runs at C++ speed. Cheers, Ralf ____________________________________________________________________________________ Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC

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Asymmetric Unit with cctbx
by Philipp Heuser 15 Jun '07

15 Jun '07

Dear all! I am not sure if this is the correct place to ask beginner-questions, how to use cctbx, but I try anyway. I would like to read in a mtz file, and convert it to a density map, which I can modify in real space using the asymmetric unit, and afterwards I would like to convert my modified map back to an mtz file. Currently I am stuck at the point, where I want to reduce the map from the unit cell to the asymmetric unit. from iotbx import mtz from cctbx import miller mtz_filename="./some_mtz_file.mtz" mtz_file = mtz.object(mtz_filename) Miller_array = mtz_file.as_miller_arrays() NEW_ARRAY=Miller_array[0].phase_transfer(Miller_array[1], deg=True) #by the way: what can I do with the mandatory_factors flag? Does grid_step=1 means the grid as a 1A spacing? FFT_map = NEW_ARRAY.fft_map(grid_step=1) Real_map = FFT_map.real_map() I would be happy, if anybody could give me some advice how to do that using the cctbx libaries! Thanks in advance Regards Philipp -- -------------------------------------------------- Dr Philipp Heuser Postdoctoral fellow EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 188 fax: +49 40 89902 149 mail: philipp.heuser(a)embl-hamburg.de --------------------------------------------------

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Re: [cctbxbb] cbflib_ext
by Ralf W. Grosse-Kunstleve 06 Jun '07

06 Jun '07

Hi Jon, Nick Sauter is working on the cbflib extension. He told me the current version is a very incomplete prototype, but that he expects to to have a more comprehensive extension around the end of this month. We are planning to move the source code (cbflib_adaptbx) to SourceForge where it will be freely available. Ralf ----- Original Message ---- From: Jon Wright <wright(a)esrf.fr> To: cctbxbb(a)phenix-online.org Sent: Thursday, May 31, 2007 4:30:38 AM Subject: [cctbxbb] cbflib_ext Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon ____________________________________________________________________________________ Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7

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cbflib_ext
by Jon Wright 31 May '07

31 May '07

Hello everypne, google has only one hit for cbflib_ext which is in marIP.py in iotbx.detectors. Any hints as to how I should find it? It does not seem to arrive in the current windows all-in download. Irrelevant perhaps, but I also had the beginnings of a swig wrapping for cbflib which is doubtless going to be incompatible with this one. Thanks, Jon

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Re: [cctbxbb] mask calculation using mmtbx
by Ralf W. Grosse-Kunstleve 04 Apr '07

04 Apr '07

Hi Celine, The interfaces have changed a lot since we published the example in the newsletter. An updated version is available here: http://cci.lbl.gov/~rwgk/tmp/example_bulk_solvent_mask_2007_04_03_1806.py This is only the mask calculation. The rest of the functionality is incorporated in the f_model.manager (I think it is explained a bit in newsletter No. 5). Let me know if you are still having trouble getting the example to work with the latest cctbx version. Ralf ____________________________________________________________________________________ Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather

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mask calculation using mmtbx
by celine Besnard 03 Apr '07

03 Apr '07

Hi, I am trying to use the cctbx to calclate a mask given a pdb following the exemple given on a newsletter. I am using a windows version of the cctbx extracted from the bundle. But in the exemple, the mask is constructed using the masks.mask_utils function from mmtbx. But I cannot see this function in mmtbx.masks. Is there another function I can use to construct a solvent mask? Thanks for any help Celine Besnard

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How can I do FFT with scitbx.fftpack in python
by 张沈鹏(电子科大大三) 29 Mar '07

29 Mar '07

which function can do fft?the help information as below?but none can do fft........... >>> help(fftpack)Help on module scitbx.fftpack in scitbx: NAME scitbx.fftpack FILE f:\foryou\桌面\fft\cctbx\cctbx_sources\scitbx\scitbx\fftpack.py FUNCTIONS adjust_gridding(...) C++ signature: adjust_gridding(int, int) -> int C++ signature: adjust_gridding(int, int, int) -> int adjust_gridding_triple(...) C++ signature: adjust_gridding_triple(class scitbx::af::small<long,10>, int) -> class scitbx::af::small<long,10> C++ signature: adjust_gridding_triple(class scitbx::af::small<long,10>, int, classscitbx::af::small<long,10>) -> class scitbx::af::small<long,10>-- Hi , I'm Earth-Man.你好，我是地球人。欢迎访问我的博客:http://zsp.javaeye.com/ --张沈鹏

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How can I do FFT with scitbx.fftpack in python
by 张沈鹏(电子科大大三) 29 Mar '07

29 Mar '07

newbie-- Hi , I'm Earth-Man.你好，我是地球人。欢迎访问我的博客:http://zsp.javaeye.com/ --张沈鹏

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Assertion Error in twin target test
by Luc Bourhis 24 Mar '07

24 Mar '07

Hi all, I have modified the least square residual classes in cctbx/xray/ targets.h and cctbx.xray to handle refinement against F^2. In the subsequent tests, the following assertion failure cropped up. It does not feel to me my changes caused it… Luc libtbx.python /Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py approx_equal eps: 0.5 approx_equal multiplier: 10000000000.0 -0.510137170481 approx_equal ERROR 0 approx_equal ERROR Traceback (most recent call last): File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 540, in <module> run() File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 488, in run tst_ls_on_i() File "/Users/luc/Developer/cctbx/cctbx_sources/cctbx/cctbx/ regression/tst_twin_target.py", line 95, in tst_ls_on_i assert approx_equal( (fdif_real-old_derivs[0][N_test])/fdif_real, 0, eps=5e-1) AssertionError

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float error
by Alexander.Schiffer＠sanofi-aventis.com 28 Feb '07

28 Feb '07

Dear all, I am trying to detwin a dataset using mmtbx.xtriage but when I run the program with the following command: mmtbx.xtriage data.mtz n_residues=1341 log=detwin.log hklout=data_detwin.mtz symmetry.action=detwin symmetry.twinning_parameters.twin_law=-h-k,k,-l twinning.twinning_parameters.fraction=0.41 I get this message: Attempting to detwin data ------------------------- Detwinning data with: - twin law: -h-k,k,-l BE WARNED! DETWINNING OF DATA DOES NOT SOLVE YOUR TWINNING PROBLEM! PREFERABLY, REFINEMENT SHOULD BE CARRIED OUT AGAINST ORIGINAL DATA ONLY USING A TWIN SPECIFIC TARGET FUNCTION! Traceback (most recent call last): File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/xtriage.py", line 5, in <module> xtriage.run(command_name="mmtbx.xtriage", args=sys.argv[1:]) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/xtriage.py", line 691, in run out=log) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/massage_twin_detwin_data.py", line 330, in __init__ self.final_array = detwinner.detwin_it(alpha=self.params.symmetry.twinning_parameters.fraction) File "/soft/ccp4/cctbx/cctbx_sources/mmtbx/mmtbx/scaling/massage_twin_detwin_data.py", line 197, in detwin_it print >> self.out, "Detwinning the data with fraction %3.2f"%(alpha) TypeError: float argument required Any idea? Best regards, Alexander Build tag: 2007_01_24_2154 Red Hat WS 3 Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH S&MA Chemical Sciences Germany Structural Biology Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w: www.sanofi-aventis.de ************************************************************************************************************************************************************** Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier (Vorsitzender), Dr. Matthias Braun, Hervé Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert **************************************************************************************************************************************************************

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Re: [cctbxbb] fractional coordinate expansion ... share occupancy
by Ralf W. Grosse-Kunstleve 07 Feb '07

07 Feb '07

Hi Andrew, > My question is what is the best method for generating the correct > distribution of atoms at these points. Naively, one would just > randomly select 30% of the shared points to be aluminums and set the > other 70% as silicon. I doubt that this is ideal. Short answer: there is nothing in the cctbx that would help you directly. I have a past as a zeolite person. My understanding was that the 30%/70% occupancy factors are a way to model spatial averages, as that's all you get from the diffraction experiment. How to handle the overlapping atoms depends highly on the context. E.g. in refinement I'd keep the overlapping atoms but constrain the coordinates to be identical. For graphical presentation I'd probably want to find a nice way to present the mixed occupancy, i.e. I wouldn't want to simply draw two crosses on top of each other. What is your context? Cheers, Ralf ____________________________________________________________________________________ Never Miss an Email Stay connected with Yahoo! Mail on your mobile. Get started! http://mobile.yahoo.com/services?promote=mail

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Re: [cctbxbb] fractional coordinate expansion ... share occupancy
by Ralf W. Grosse-Kunstleve 06 Feb '07

06 Feb '07

Hi David, > I have provided an example compound with scatterer code below as you > will note the output has overlapping atoms and the resulting 58 points > are not enough to cover the chemical formula. What do I need to do to > fix this? Sorry, I don't understand the question. Could you please explain what you expect to see as the output? Ralf ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL

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fractional coordinate expansion ... share occupancy
by David A Carr 03 Feb '07

03 Feb '07

Hello All, Thanks to Ralph's modification in January I have had success with cctbx. Now I have another question. Is there a method in the cctbx for dealing with shared occupancy coordinates? I have a compound where in the reduced cell the x,y,z coordinates for two different atoms are the same and a "sof" fraction is given. What is the best practice for handling such points? I have provided an example compound with scatterer code below as you will note the output has overlapping atoms and the resulting 58 points are not enough to cover the chemical formula. What do I need to do to fix this? Thanks, Andrew **************************************** Dr. D. Andrew Carr George Mason University dcarr2(a)gmu.edu ## ## The following example is ## Na9.52 (Al7.2 Si16.8 O48) (H2 O)5.88 ## DAC 1.12.07 ##--------------------------------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex def demo(): crystal_symmetry = crystal.symmetry( unit_cell="13.12,13.57,15.81,90.0,143.0,90.000000", space_group_symbol="C 1 2/m 1") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer(#element = "Si", label="Si1", site=(0.0042,0.2561,0.0965),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al1", site=(0.0042,0.2561,0.0965),occupancy=0.3)) scatterers.append(xray.scatterer(#element = "Si", label="Si2", site=(0.3442,0.1125,0.3278),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al2", site=(0.3442,0.1125,0.3278),occupancy=0.3)) scatterers.append(xray.scatterer(#element = "Si", label="Si3", site=(0.3497,0.1193,0.1355),occupancy=0.7)) scatterers.append(xray.scatterer(#element = "Al", label="Al3", site=(0.3497,0.1193,0.1355),occupancy=0.3)) #--------------------------------------------- # Oxygens #--------------------------------------------- scatterers.append(xray.scatterer(#element = "O", label="O1", site=(0,0.3203,0))) scatterers.append(xray.scatterer(#element = "O", label="O2", site=(0.4292,0.1372,0.2924))) scatterers.append(xray.scatterer(#element = "O", label="O3", site=(-.0283,0.3315,0.1491))) scatterers.append(xray.scatterer(#element = "O", label="O4", site=(0.5,0.1347,0.5))) scatterers.append(xray.scatterer(#element = "O", label="O5", site=(0.1993,0.2072,0.2422))) scatterers.append(xray.scatterer(#element = "O", label="O6", site=(0.308,0,0.0850))) scatterers.append(xray.scatterer(#element = "O", label="O7", site=(-.1454,0.1619,0.0205))) scatterers.append(xray.scatterer(#element = "O", label="O8", site=(0.256,0,0.289))) scatterers.append(xray.scatterer(#element = "Na", label="Na", site=(0.7235,0.2619,0.3904),occupancy=1.19)) scatterers.append(xray.scatterer(#element = "O", label="O9", site=(0.663,0.5645,0.7249),occupancy=0.47)) scatterers.append(xray.scatterer(#element = "O", label="O10", site=(0.304,0,0.686),occupancy=0.53)) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) icsd_structure.show_summary().show_scatterers() print icsd_structure.show_distances(distance_cutoff=2.5) print primitive_structure = icsd_structure.primitive_setting() primitive_structure.show_summary().show_scatterers() print p1_structure = primitive_structure.expand_to_p1() p1_structure.show_summary().show_scatterers() print print "OK" if (__name__ == "__main__"): demo()

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Re: [cctbxbb] set_use_u_iso and set_use_u_aniso
by Ralf W. Grosse-Kunstleve 09 Jan '07

09 Jan '07

> > What are those methods of xray.scatterer for? > > And what are their relation to set_grad_u_iso and set_grad_u_aniso? You can use any combination of u_iso and u_star (anisotropic). We had to make this generalization to accomodate TLS refinement. I.e. there are four combinations, use_u_iso/use_u_aniso false/false, true/false, false/true, true/true. The total Debye-Waller factor is the product dw_iso * dw_aniso. If use_u_iso is false, dw_iso = 1, similarly dw_aniso = 1 if use_u_ansio is false. Unfortunately I didn't find the time yet to eliminate the anisotropic_flag, which is redundant. The main problem is that phaser needs to be changed in many places in order to get rid of the flag. The grad_u_iso and grad_u_ansio control the computation of the gradients. The flags are independent of corresponding use flags. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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set_use_u_iso and set_use_u_aniso
by Luc Bourhis 08 Jan '07

08 Jan '07

What are those methods of xray.scatterer for? Luc

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Re: [cctbxbb] Error in fractional coordinates returned by cctbx
by Ralf W. Grosse-Kunstleve 29 Dec '06

29 Dec '06

> We could add .mod_positive() and .mod_short() methods to flex.xray_scatterer, and > then the corresponding two-liners .sites_mod_positive() and .sites_mod_short() to > xray.structure. I'll put it on my to-do list. Done: http://cci.lbl.gov/cctbx_build/all.html Build 2006_12_28_2147 or later includes the new methods. E.g.: p1_structure = structure.expand_to_p1().sites_mod_positive() HTH, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [cctbxbb] Error in fractional coordinates returned by cctbx
by Ralf W. Grosse-Kunstleve 29 Dec '06

29 Dec '06

> flex.fmod_positive( coordinates, 1 ) > > on the fractional coordinates on your sites. > > Ralf, is there a better way? No, Peter's Python loop over the scatterers is currently the best solution. We could add .mod_positive() and .mod_short() methods to flex.xray_scatterer, and then the corresponding two-liners .sites_mod_positive() and .sites_mod_short() to xray.structure. I'll put it on my to-do list. Cheers, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Error in fractional coordinates returned by cctbx
by David A Carr 29 Dec '06

29 Dec '06

Hello, I have encountered the following inconsistency when working with cctbx. The compound I am working with is as follows. #Silicon Dioxide Quartz low. #Si O2 #ICSD Coll Number 62410 label="Si", site=(0.4643,0.0,0.6667) label="O", site=(0.411,0.2773,0.7783) unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0", space_group_symbol="P 32 2 1" The error is can be seen in the below. In the second and third Si lines the z value is not a fraction of the unit. Similarly two of the oxygens are placed outside the unit cell. Why does cctbx place these outside of the unit cell? Number of scatterers: 9 At special positions: 0 Unit cell: (4.843, 4.843, 5.348, 90, 90, 120) Space group: P 1 (No. 1) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si1 Si 1 ( 0.4643 0.0000 0.6667) 1.00 0.0000 Si1 Si 1 ( 0.0000 0.4643 1.3333) 1.00 0.0000 Si1 Si 1 (-0.4643 -0.4643 1.0000) 1.00 0.0000 O1 O 1 ( 0.4110 0.2773 0.7783) 1.00 0.0000 O1 O 1 (-0.2773 0.1337 1.4450) 1.00 0.0000 O1 O 1 (-0.1337 -0.4110 1.1116) 1.00 0.0000 O1 O 1 ( 0.1337 -0.2773 -0.4450) 1.00 0.0000 O1 O 1 (-0.4110 -0.1337 -0.1116) 1.00 0.0000 O1 O 1 ( 0.2773 0.4110 -0.7783) 1.00 0.0000 Below shows the expected fractional coordinates as expected. Based on the space group P 32 2 1. 0.4643 0.0000 0.6667 0.0000 0.4643 0.3333 -0.4643 -0.4643 0.0000 0.4110 0.2773 0.7783 -0.2773 0.1337 0.4450 -0.1337 -0.4110 0.1116 0.1337 -0.2773 -0.4450 -0.4110 -0.1337 -0.1116 0.2773 0.4110 -0.7783 Any insight into this would be of help. I am hoping to use cctbx as a part of our current software development project. Thanks, D.Andrew Carr dcarr2(a)gmu.edu # Below is the code that generates the error # posted above. #--------------------------------------------------- from cctbx import xray from cctbx import crystal from cctbx.array_family import flex def demo(): crystal_symmetry = crystal.symmetry( unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0", space_group_symbol="P 32 2 1") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer( label="Si", site=(0.4643,0.0,0.6667))) scatterers.append(xray.scatterer( label="O", site=(0.411,0.2773,0.7783))) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) print "ICSD Structure" icsd_structure.show_summary().show_scatterers() print icsd_structure.show_distances(distance_cutoff=2.5) print "Primitive" primitive_structure = icsd_structure.primitive_setting() primitive_structure.show_summary().show_scatterers() print p1_structure = primitive_structure.expand_to_p1() p1_structure.show_summary().show_scatterers() print print "Expanded to P1" icsd_structure.expand_to_p1().show_summary().show_scatterers() print "OK" if (__name__ == "__main__"): demo()

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Re: [cctbxbb] Possible contributions to the cctbx
by Luc Bourhis 16 Dec '06

16 Dec '06

On 16 Dec 2006, at 06:53, Ralf W. Grosse-Kunstleve wrote: >> We have not developed those two features yet. Fair enough about the >> smtbx… We can easily mimic the mmtbx, > > I just wanted to say that you are most welcome to start the smtbx > tree under the cctbx SF probject. This is just an offer, I'd be > just as happy if you decide to start the tree somewhere else. Oh, I see! Sorry, I misunderstood you then. Thanks for the offer. It would make sense indeed. Of course, our ultimate goal is to develop the equivalent of Phenix for small molecules, and that would not live on sourceforge.net/projects/cctbx either. > It is technically very easy to leverage the cctbx build system for > other modules (I have at least 20 other modules floating around), > i.e. so that you can say libtbx/configure.py smtbx and you'll have > everything set up (PYTHONPATH, PATH, smtbx.python, etc.). The > problem is it is not documented enough (just Michael > Hohn's notes at http://cci.lbl.gov/~hohn/scitbx-tour.html). I hope > to find time to write more detailed web pages over the holiday break. I would highly appreciate that. By easy you probably mean it boils down to add a few instructions in a config file but my experience is that finding out those in the first place is not easy! Anyway, I am afraid I will come back to you with countless questions when I will start to develop with the cctbx. Thanks again, Luc

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Re: [cctbxbb] Possible contributions to the cctbx
by Ralf W. Grosse-Kunstleve 16 Dec '06

16 Dec '06

Hi Luc, > This is a spin-off from the thread about constrained hydrogen > refinement. On the todo list of our EPSRC project, we have a few more > items which I think would fit well in the cctbx. > > 1) anharmonic thermal displacements. Not only the Gram-Charlier ones > but also about the modelling of atoms disordered over a circle or a > line (as done in Crystals [1]). > > 2) multipolar scattering factors, for charge density studies. These suggestions look quite specific to small molecule crystallography. They make me think it would be best to have a "smtbx" (small molecule toolbox) module (inspired by David's message). Do you have a CVS or SVN repository already? Is it publicly accessible (read only)? Cheers, Ralf __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [cctbxbb] constrained hydrogen geometry
by Ralf W. Grosse-Kunstleve 15 Dec '06

15 Dec '06

Hi Luc, > I was trying to figure out whether this interface would be sufficient > and/or necessary for the Hydrogen geometry constraints. I am not > quite sure I understand what is gradient_sum_matrix exactly in fact. gradient_sum_matrix is not directly relevant to the hydrogen problem. The only commonality is the chain rule. Roughly, if you have to variables x, y which are "normally" independent and have gradients df/dx and df/dy, and if under "special circumstances" x becomes a function of y (or vice versa), you have to add up the gradients according to the chain rule. If you work this out for the linear relations given by the symmetry operations, you can cast the result in the form of the "gradient sum matrices". Below is a simple example, by Peter Zwart, constraining the sum of occupancies to one. In the hydrogen case, I'd think you just write down the equations constraining the coordinates to each other. Then study them to apply the chain rule. Done! :) Regarding the interfaces: I usually think about interfaces after I've worked out the math and/or algorithms. It is good to make interfaces as similar as possible, but ultimately "form follows function", as a famous architect taught us. Most importantly, find class, function and variable names that convey meaning even to the "reader" no immersed in the problem. That's more than half the battle. > It is the philosophy of the cctbx, isn't it? You have constructed > the cctbx so as to use it as Python library, relegating C++ to some > sort of assembly language for efficiency. Yes, that's a good viewpoint. > The lack of abstraction in the C++ code of the cctbx I don't know what you mean. :) > (hardly any inheritance, Because it has a large potential for obfuscating what's going on. Inheritance is like salt in the soup. > no advanced genericity) You must have overlooked Boost.Python. :) If that doesn't change your mind, look closer at the implementation of the array algebra header files in scitbx/array_family, including the auto-generated header files in cctbx_build/include. > would require wrapping a lot of the cctbx classes behind > proxies inheriting from abstract types. I find this approach cumbersome and fruitless. I am a big believer in form follows function. Function follows form (design interfaces first) doesn't work for me. I always try to achieve first what I actually want to do, then find a good form for it. > A typical example for me are those classes dealing > with position constraints and ADP constraints. They > are unrelated in C++, cctbx::sgtbx::site_constraints and > cctbx::sgtbx::tensor_rank_2::constraints, although they have both have > the same member functions listed above. Functionally the member functions are unrelated, unless you can come up with a general engine that applies the chain rule automatically to a given function. (Such tools exist, e.g. adolc, but are heavy-duty.) I think it would be counter-productive to tie adp/site constraints code together just because the names of the methods are similar. I consider modularity a more important value. > Of course, from Python, it does not matter, thanks to duck typing: > if two objects answer the same method calls, then they are by all > practical means of the same type. The adp/site constraints are not a good example. We don't want to use them interchangeably. I've tried to use the "functor" idea (unifies interfaces without inheritance) in some places, but even that often turns out to be a struggle. This is especially the case when another person adds on (e.g. cctbx.xray.target_functors). What counts the most in my opinion is to avoid redundancy. That's my most important goal when writing source code, because redundancy hampers progress and multiplies bugs, among other bad things. I'm trying to use all tools available to cut back redundancy. I find both templates and inheritance invaluable and use them where they help reducing redundancy, but I do not see "use templates" or "use inheritance" as goals in their own right. > Our group would be more than happy to contribute them to the cctbx > since we absolutely need them for our project. That's great! I think you can achieve a lot quickly if you limit yourself initially to Python. If you then check in what you have, I'd be happy to walk you through the first few times moving time-critical functionality to C++. Cheers, Ralf By Peter Zwart: Some ideas on how to restrain sums of variables to unity. say we have f(a,b,c) with a(x1) = x1 b(x2) = x2 c(x1,x2) = 1 - x1 - x2 Say we have from the refinement engine the following numerical values (right hand side) for our partial derivatives: df/da = Ga df/db = Gb df/dc = Gc The chain rule says: dq/dx = (dq/du)(du/dx) + (dq/dv)(dv/dx) Thus df/dx1 = (df/da)(da/dx1) + (df/dc)(dc/dx1) = Ga - Gc df/dx2 = (df/db)(db/dx2) + (df/dc)(dc/dx2) = Gb - Gc This gives you the rule to go from the full set of derivatives to the reduced set of derivatives (for the general case): #-------------------------------------------------- def pack_derivatives( g_array ): result = g_array[0:g_array.size()-1 ] result = result - g_array[ g_array.size()-1 ] return result #-------------------------------------------------- You also need to go from a reduced set of parameters to the full set of parameters (for the general case): #-------------------------------------------------- def expand_parameters( x ): result = x.deep_copy() result = result.append( 1 - flex.sum(x) ) return result #-------------------------------------------------- This of course assumes that the 'last' variable is the non unique none during refinement. ____________________________________________________________________________________ Any questions? Get answers on any topic at www.Answers.yahoo.com. Try it now.

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Possible contributions to the cctbx
by Luc Bourhis 15 Dec '06

15 Dec '06

This is a spin-off from the thread about constrained hydrogen refinement. On the todo list of our EPSRC project, we have a few more items which I think would fit well in the cctbx. 1) anharmonic thermal displacements. Not only the Gram-Charlier ones but also about the modelling of atoms disordered over a circle or a line (as done in Crystals [1]). 2) multipolar scattering factors, for charge density studies. [1] L. Schröder, D.J. Watkin, A. Cousson, R.I. Cooper, and W. Paulus. Crystals enhancements: refinement of atoms continuously disordered along a line, on a ring or on the surface of a sphere. J. Appl. Cryst., 37:545–550, 2004. Best wishes, Luc

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Re: [cctbxbb] constrained hydrogen geometry
by Ralf W. Grosse-Kunstleve 15 Dec '06

15 Dec '06

Hi Luc, > I have not been able to find any facility to constraint hydrogen > geometry, in the manner of the AFIX in ShelXL I mean. Have I missed > them or would it need to be implemented? They need to be implemented. > In the latter case, I have tried to figure out how this could be > done. I manage to find how position and ADP constraints are handled > by constraint objects featuring methods to return the independent > variables and the gradient with respect to them. Then cctbx/cctbx/ > examples/structure_factor_derivatives_4.py shows how those features > can be used. Would Hydrogen geometry constraint be best handled by > mimicking those special positions constraint? I am not sure. The handling of hydrogens seems more complicated than dealing with the constraints due to symmetry. I just had a quick look at the SHELX manual. I see many special cases. If I had a chance to work on this, I'd start with a Python script emulating some of the cases handled by SHELX, refining a few small structures. After getting a few concrete examples to work, I'd try to generalize the procedures for handling the special cases. I'd switch to C++ only after having fully conquered the math and the bookkeeping in Python, and being sure about the final interfaces. To implement the core refinement, I'd copy and modify cctbx/cctbx/xray/minimization.py. See also phenix/phenix/substructure/hyss/minimization.py, which you can find in the CCI Apps bundle (http://phenix-online.org/download/cci_apps/). Hope this helps. As you can tell, I am not an expert in constrained hydrogen refinement, but I'm very interested in seeing such algorithms in the cctbx (we'd probably want to use them in phenix.refine). Let me know if you feel I can do something to help out. Cheers, Ralf ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com

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constrained hydrogen geometry
by Luc Bourhis 14 Dec '06

14 Dec '06

I have not been able to find any facility to constraint hydrogen geometry, in the manner of the AFIX in ShelXL I mean. Have I missed them or would it need to be implemented? In the latter case, I have tried to figure out how this could be done. I manage to find how position and ADP constraints are handled by constraint objects featuring methods to return the independent variables and the gradient with respect to them. Then cctbx/cctbx/ examples/structure_factor_derivatives_4.py shows how those features can be used. Would Hydrogen geometry constraint be best handled by mimicking those special positions constraint? Cheers, luc

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Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 12 Dec '06

12 Dec '06

> I believe Ralph can handle C-1 Yes, most definitely. There are no rational rotation matrix elements => no problem. > In each pair of tables 4 & 5 and 6 & 7 atomic parameters can be > compared directly. If the P to C transformation is made, all four > tables can be compared by inspection. I believe you can always achieve this even with the cctbx as is. You just may have to transform both structures to some unusual setting. Consider that matrices with rational rotation parts elements are not only relatively expensive to handle, but the corresponding geometry is also highly non-intuitive. I.e. if you transform both structures to avoid the rational rotation parts I bet the comparison is easier to explain and understand. The usual trick is to use space_group_type to go to reference settings, then .niggli_cell() to go to primitive settings, then deal with the extra translations in the primitive settings. Technically it comes down to combining the change-of-basis matrices in the right way, which is easy. > In this case, the referees and editors refused to accept a non standard > SG, so the text of the paper becomes laborious, explaining what would > otherwise have been obvious. If you give change-of-basis matrices from the reference setting (using space_group_type) I think it should be easy to argue the case for presenting the comparison using a convenient frame of reference. Note that the space_group_type has a ".universal_hermann_mauguin_symbol()" method to produce "nice" general space group symbols for any setting that can be handled by the space_group class. We use this in the automatic generation of subgroup graphs. E.g. try this: iotbx.explore_metric_symmetry --unit-cell "68.4 68.4 68.3 109.5 109.4 109.5" --space-group=p1 --graph graph.png For this to work you need graphviz (open source). If you don't have it, here is the resulting png file: http://cci.lbl.gov/~rwgk/tmp/explore_metric_symmetry_graph.png > In higer symmetry SGs it may be easier to compare structures if even more > bizzare SG are invented, or if non-standard origins are used. I don't think it is a problem if you use the right existing tools. :) > Im sure this will be true, and that someone will provide the > user-interface for generating the basis vectors form the new (probably > enlarged) cell and new atomic parameters after the expansion. I'd be happy to help integrate the required additions. > Im sure the SM-tbx folk have more pressing problems to deal with than > worrying about this minority application The core "cctbx" (the module, not the project, see Comp. Comm. Newsletter No. 1) is meant to be a small-molecule toolbox. Please don't view it as "read only", unless you don't want to release your additions as open source. (?) Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

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Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 11 Dec '06

11 Dec '06

Hi Luc, > If I understand correctly, space_group_type lets the user use any > space-group in a non-standard setting defined by a special change of > basis. space_group_type determines the change-of-basis matrix from a given setting to the reference setting. > Now your example would require the matrix of change of basis > to be rational whereas in the current implementation it can only be > integral. The change_of_basis_op class has both rational rotation and rational translation parts, with a common r_den for the 9 rotation matrix elements, and a common t_den for the 3 translation vector elements. The "r_den" is fixed at 1 only for the space_group class. Since space_group_type operates only on space_group objects, the limitation applies here too, but the resulting change-of-basis rotation parts certainly don't have to be integral (that would be a terrible limitation). > At least as far as I understand, from the code and your > comments. Thus, the only place where rational numbers would be > necessary is in those matrices of change of basis, isn't it? Now, > would it be possible to define a new class > space_group_irrational_setting which would provide services very > similar to space_group_type but accepting non-integral matrices for > the change of basis? You are correct. If you need to handle space groups with rational rotation matrices, the way forward is to implement a new class similar to space_group (I'd go for space_group_rational) with a little bit of cut-and-paste to replicate the group multiplication. However, I don't think it is worth redoing the entire space_group_type implementation to accommodate rational rotation parts. In fact, I think it would be a bad solution because of the runtime impact. Consider that any space group when transformed to the primitive setting will have only integral rotation matrices. I.e. all you need is an algorithm that figures out an "initial" change-of-basis matrix to a (any) primitive setting. Construct a standard space_group object with the transformed symmetry operations and feed it into space_group_type. Multiply the "initial" change-of-basis with the output of space_group_type, done. This way you get the desired generality with a moderate effort, without impacting the performance of the many established algorithms based on space_group. Cheers, Ralf ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited

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Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 11 Dec '06

11 Dec '06

> Luc, This is a key item in Ralphs reply: > > "You cannot change the rotation denominator (fixed at 1) for the > matrices processed by sgtbx.space_group. Therefore you cannot work > with, e.g. the pseudo-orthorhombic C-centered setting of a hexagonal > space group. However, I never came across a situation where this > was interesting." > > If the design of the toolbox is too restrictive to permit the user to > invent any closed set of operators they want - well thats the end of it. > As we say in the UK, C'est la vie. Could you please outline a plausible example where the current implementation is a serious limitation? > There were lots of things we would have liked to add to CRYSTALS, but > there was no room in Bob Carruthers database, and extending it would > have been a major hasle. I am sure the cctbx is more flexible. > As you pointed out, there are work-arounds that can be applied by a > clever crystallographer, and the less clever ones won't even try to do > anything clever. It's a self-limiting situation! Much of what crystal > enginners want could be done if Oleg lets the user create an extended > atom parameter list, and put this into a new unit cell in P1. You can create any P1 cell you want, it is totally trivial: first use e.g. xray_structure.expand_to_p1(), then loop over the translations you want to duplicate the atoms. We can easily add methods to do it in one call. Note that the cctbx is open source, with the possibility of write access to the main source repository. Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

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Re: [cctbxbb] Fail to extend space-group with centring translations
by Ralf W. Grosse-Kunstleve 11 Dec '06

11 Dec '06

Hi Luc, You can make both examples work like this: from cctbx.sgtbx import * info = space_group_info("P2/a") g = info.group() g.expand_ltr(tr_vec((1,1,1),2).new_denominator(sg_t_den)) from cctbx import sgtbx s = sgtbx.space_group_symbols("P21/c") g = sgtbx.space_group(s) g.expand_ltr(sgtbx.tr_vec((1,0,1),3).new_denominator(sg_t_den)) g.expand_ltr(sgtbx.tr_vec((2,0,2),3).new_denominator(sg_t_den)) Any setting of any crystallographic space group can be processed via sgtbx.space_group, as long as the rotation matrix elements are integers. You may just have to be careful in choosing appropriate "t_den" (translation denominators). All matrices in a given space_group instance have to have the same t_den. I know it can be a hassle, but I don't consider it a practical limitation. Note that sg_t_den is just the default (12). You can set other values if necessary. You cannot change the rotation denominator (fixed at 1) for the matrices processed by sgtbx.space_group. Therefore you cannot work with, e.g. the pseudo-orthorhombic C-centered setting of a hexagonal space group. However, I never came across a situation where this was interesting. It would be possible to rewrite the sgtbx based on boost::rational<int>, but it is a big project. The advantage would be more flexibility, the disadvantage a performance decrease. If there is a strong reason I would go for more flexibility, but so far I've never found this worthwhile. BTW: A more convenient way of adding symmetry operations is: g.expand_smx("x+1/2,y+1/2,z+1/2") Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

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Fail to extend space-group with centring translations
by Luc Bourhis 09 Dec '06

09 Dec '06

Hello there, with the latest cctbx release, the following Python snippet fails from cctbx.sgtbx import * info = space_group_info("P2/a") g = info.group() g.expand_ltr(tr_vec((1,1,1),2)) The exception indicates that it is not possible to add a centring translation with a denominator of 2 to a group which does not have any centring translations with that denominator. Of course, in that case, that description is trivial because P2/a does not have any centring translations! My real intent was actually to introduce 1/3 centring translations so as to deal with a tripled cell. I am just citing the example above to show the extent of the problem. My original, failing, snippet was therefore from cctbx import sgtbx s = sgtbx.space_group_symbols("P21/c") g = sgtbx.space_group(s) g.expand_ltr(sgtbx.tr_vec((1,0,1),3)) g.expand_ltr(sgtbx.tr_vec((2,0,2),3)) It fails with the same class of exception. It seems like it is a deeply rooted limitation and that brings me to the bigger picture. I am currently working on an EPSRC grant to write the next generation of small molecule crystallographic software, a joint collaboration between Judith Howard in Durham and David Watkin in Oxford (all in UK, just in case…!). The CCTBX is obviously a seducing foundation for such a project. Thus we have tried to push it into corners which do actually matter to a significant minority of small molecule crystallographers. So I would like to know how difficult it would be to lift the limitation at hand. Would it trigger a cascade of changes throughout the sgtbx? Luc Bourhis

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Obtaining symmetry information
by Konrad Hinsen 04 Dec '06

04 Dec '06

Dear All, I am trying to reconstruct an entire unit cell from an cctbx.xray.structure object that contains the scatterers in the asymmetric unit. Ideally, I'd call a method that does the work for me, but at least I would like to obtain a list of the symmetry transformations that must be applied. That information must be somewhere in there... but where? Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen(a)cnrs-orleans.fr ---------------------------------------------------------------------

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compiling problem with latest cctbx on OS X
by William Scott 30 Aug '06

30 Aug '06

With Ralf and Erik's help and advice, (cf http://www.phenix- online.org/pipermail/cctbxbb/2005-September/thread.html ) I made a Mac OS X fink package for the cctbx source release. http://pdb.finkproject.org/pdb/search.php?summary=cctbx Everything works fine on OS X v. 10.4, gcc 4.0.1, on both ppc and intel platforms, until today when I realized the package I made is now out of date (as of July I think). I'm now having problems compiling the latest version. I've put the log file here: http://xanana.ucsc.edu/~wgscott/kipaut/fink/compile.log Briefly, I think the failure is taking place here: c++ -o cctbx/translation_search/boost_python/fast_nv1995.o -c -fPIC - no-cpp-precomp -ftemplate-depth-130 -Wno-long-double -w - DBOOST_DISABLE_THREADS -DNDEBUG -O3 -ffast-math - DBOOST_PYTHON_MAX_BASES=2 -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/boost -Iinclude -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/cctbx/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources/scitbx/include -I/sw/src/fink.build/cctbx-60705-1001/ cctbx_sources -I/Library/Frameworks/Python.framework/Versions/2.4/ include/python2.4 /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/ cctbx/translation_search/boost_python/fast_nv1995.cpp /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/scitbx/include/ scitbx/fftpack/complex_to_complex.h: In member function 'void scitbx::fftpack::complex_to_complex<RealType, ComplexType>::pass3 (scitbx::fftpack::select_sign<Tag>, size_t, size_t, RealType*, RealType*, const RealType*, const RealType*)': /sw/src/fink.build/cctbx-60705-1001/cctbx_sources/scitbx/include/ scitbx/fftpack/complex_to_complex.h:361: error: expected unqualified- id before numeric constant Any suggestions? Thanks. Bill Scott

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Generate atom data from cctbx
by Jen-Chang Chen 16 Jan '06

16 Jan '06

Dear Sirs, I have installed "cctbx" in my Linux box and ran the examples,e.g. the beach in the box and the Cr2O3 case demonstrated in the mailing list, successfully. I'd like to apply cctbx as a generator of the crystallographic data. Based on the ICSD database, I can obtain a crystal structure of a mineral. Would it be possible to print out all atom positions in a unit cell or a supercell using cctbx? Thank you very much. Sincerely, Jen-Chang "James" Chen

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Re: [cctbxbb] Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 26 Nov '05

26 Nov '05

Thanks for your script. I am doing this in C++. I can't find a xray::structure class in the C++ documentation. Does this only exist in Python ? Nevertheless, I run your script in Python and the result is somewhat different from what I get, but I still think it is wrong. If I create and visualize a supercell from the coordinates given by the script (e. g., with gdis) I no longer see the hexagonal arrangement of the atoms typical for the conventional cell. Since the conversion from conventional to primitive cell should only redefine the cell but not the atom positions (in Cartesian coordinates) I believe the output is incorrect. Best Regards, Jörg-Rüdiger Hill >--- J?rg-R?diger Hill <Joerg-Ruediger.Hill(a)scienomics.com> wrote: >> Dear All, >> I am trying to convert from a conventional cell to a primitive cell using >> cctbx, but I am having some problems. > >Are you doing this in C++ or in Python? > >> What I do is the following: >> 1) I construct a spaceGroup object using the space group symbol >> 2) I retrieve the change of basis operator using z2p_op() from the space >> group object >> 3) I apply this operator to the conventional cell >> 4) I take a list of symmetry unique atoms and apply the operator to their >> fractional coordinates >> At this point I have a primitive cell which agrees exactly with what I get >> from other codes. > >Note that there are ambiguities in the choice of the change-of-basis operator >to the primitive cell. You may get different results from different programs, >which are all correct. It is a coincidence if you get the same result. > >> The problem comes when I am trying to construct all atoms >> from the symmetry unique ones. I do this by the following procedure: >> 5) I take the space group object and call its change_basis() method with >> the z2p_op() operator >> 6) I loop over all order_z() symmetry operations in the space group >> applying the operation to the fractional coordinates making sure that I >> don't create two atoms at the same position > >You could use the site_symmetry and sym_equiv_sites classes to deal with the >special positions. > >> The whole procedure works well, e. g., for cubic crystals. However, if I >> take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps >> 5 and 6 above is not correct. In this case the conventional cell has a=b != >> c, >> alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and >> alpha=beta=gamma. > >That's what I'd expect. > >> I have tried to add ":R" to the space group symbol and >> constructing a new spaceGroup object in step 5 above, but that does not >> make any difference. What do I have to do to build the crystal in this case >> or what is wrong with my procedure ? > >Attached is a copy of the new cctbx/cctbx/examples/cr2o3_primitive_cell.py >script (in the CVS already; will also be in the next set of auto-build >bundles). Could you please compare your results to the output of this script? > >The script shows a high-level implementation. I could add a lower-level >equivalent that is more in line with what you'd do in C++. Let me know if > this is what you need. > >Cheers, > Ralf > > >from cctbx import xray >from cctbx import crystal >from cctbx.array_family import flex > >def demo(): > """ > Result of ICSD query: > N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000) > C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000 > S GRUP R -3 C > A Cr1 0.000000 0.000000 0.347570 0.000000 > A O1 0.305830 0.000000 0.250000 > """ > crystal_symmetry = crystal.symmetry( > unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000", > space_group_symbol="R -3 C") > scatterers = flex.xray_scatterer() > scatterers.append(xray.scatterer( > label="Cr1", site=(0.000000,0.000000,0.347570))) > scatterers.append(xray.scatterer( > label="O1", site=(0.305830,0.000000,0.250000))) > icsd_structure = xray.structure( > crystal_symmetry=crystal_symmetry, > scatterers=scatterers) > icsd_structure.show_summary().show_scatterers() > print > icsd_structure.show_distances(distance_cutoff=2.5) > print > primitive_structure = icsd_structure.primitive_setting() > primitive_structure.show_summary().show_scatterers() > print > p1_structure = primitive_structure.expand_to_p1() > p1_structure.show_summary().show_scatterers() > print > print "OK" > >if (__name__ == "__main__"): > demo() -- ------------------------------------------------------------------------------- Dr. Jörg-Rüdiger Hill Tel.: +33 1 53 43 51 05 Director R & D Tel. (direct): +49 89 613 05 700 Scienomics Fax: +33 1 53 43 92 92 17 Square Edouard VII E-Mail: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 25 Nov '05

25 Nov '05

Dear All, I am trying to convert from a conventional cell to a primitive cell using cctbx, but I am having some problems. What I do is the following: 1) I construct a spaceGroup object using the space group symbol 2) I retrieve the change of basis operator using z2p_op() from the space group object 3) I apply this operator to the conventional cell 4) I take a list of symmetry unique atoms and apply the operator to their fractional coordinates At this point I have a primitive cell which agrees exactly with what I get from other codes. The problem comes when I am trying to construct all atoms from the symmetry unique ones. I do this by the following procedure: 5) I take the space group object and call its change_basis() method with the z2p_op() operator 6) I loop over all order_z() symmetry operations in the space group applying the operation to the fractional coordinates making sure that I don't create two atoms at the same position The whole procedure works well, e. g., for cubic crystals. However, if I take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps 5 and 6 above is not correct. In this case the conventional cell has a=b != c, alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and alpha=beta=gamma. I have tried to add ":R" to the space group symbol and constructing a new spaceGroup object in step 5 above, but that does not make any difference. What do I have to do to build the crystal in this case or what is wrong with my procedure ? Best Regards, Jörg-Rüdiger Hill -- ------------------------------------------------------------------------------- Dr. Jörg-Rüdiger Hill Tel.: +33 1 53 43 51 05 Director R & D Tel. (direct): +49 89 613 05 700 Scienomics Fax: +33 1 53 43 92 92 17 Square Edouard VII E-Mail: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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mmtbx source tree moved to SourceForge CVS
by Ralf W. Grosse-Kunstleve 25 Oct '05

25 Oct '05

Today we've finally moved the mmtbx source tree from our private CVS server (cci.lbl.gov) to SourceForge. **** Old working copies checked out from cci.lbl.gov are no longer valid and should be removed. **** To check out a new working copy from SourceForge: Developer access: cvs [email protected]:/cvsroot/cctbx co -P mmtbx replace "user" with your SourceForge user name. Anonymous access: cvs -d:pserver:[email protected]:/cvsroot/cctbx co -P mmtbx It may take a few hours before the anonymous access is available and before the mmtbx tree is visible in the viewcvs web interface. For the records: we were hesitant to move more source trees to SourceForge because the CVS server was often heavily overloaded; a cvs update could take a significant amount of time. However, a recent hardware upgrade at SourceForge has improved performance dramatically. Performance has been very good for a couple of months. Therefore we feel it is a good opportunity to finally move the mmtbx sources to the proper place. This way, browsing the tree via viewcvs is available to everybody, and the automatic archiving of cvs activities (via email) should now work reliably for all developers. Cheers, Ralf __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

1 0

strange silicon
by Marc Gailhanou 18 Oct '05

18 Oct '05

Hello, I have some trouble with cctbx, I try to understand why and I do not succeed. I need your help ! I replaced quartz with silicon in the "beach in the box" example/tutorial. This is the resulting code : from cctbx import xray from cctbx import crystal from cctbx.array_family import flex silicon_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.4307,5.4307,5.4307,90,90,90), space_group_symbol="Fd3m")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(0.,0.,0.), u=0) ])) silicon_structure.show_summary().show_scatterers() for scatterer in silicon_structure.scatterers(): print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site site_symmetry = silicon_structure.site_symmetry(scatterer.site) print " point group type:", site_symmetry.point_group_type() print " special position operator:", site_symmetry.special_op() f_calc = silicon_structure.structure_factors(d_min=1).f_calc() f_calc.show_summary().show_array() and running the script gives the following result result : Number of scatterers: 1 At special positions: 1 Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si Si 16 ( 0.0000 0.0000 0.0000) 1.00 0.0000 Si: 0.0000 0.0000 0.0000 point group type: -3m special position operator: 0,0,0 Miller array info: None Observation type: None Type of data: complex_double, size=9 Type of sigmas: None Number of Miller indices: 9 Anomalous flag: False Unit cell: (5.4307, 5.4307, 5.4307, 90, 90, 90) Space group: F d -3 m :2 (No. 227) (0, 2, 2) 0j (0, 4, 0) (120.217658126+0j) (1, 1, 1) (-84.1884955081+0j) (1, 3, 1) (65.4837172721+0j) (1, 3, 3) (57.4543830832+0j) (1, 5, 1) (-51.4875968695+0j) (2, 2, 2) (128.545406989+0j) (2, 4, 2) 0j (3, 3, 3) (-51.4875968695+0j) The 220 structure factor, at least, does not look correct . I do not understand the 16 multiplicity either. Is there something I miss ? Best regards Marc

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Re: [cctbxbb] differing build and install directories?
by Ralf W. Grosse-Kunstleve 29 Sep '05

29 Sep '05

Hi Bill, Sorry that I dropped the ball on this question before. Erik outlines the best way of creating a portable cctbx bundle, but in this case there may be a simpler alternative: - simply cp -r the installation into the final destination - re-run python .../libtbx/configure.py mmtbx in the new build directory location. This will update all full paths. Note though that this simple approach will preserve all intermediate files created by the build procedure (i.e. all the .o files and some auto-generated C++ files). But please try this out first. If it does what you want we can think about ways of getting rid of the unwanted files. > The other issue is that I need to hard-code in the DYLIB path I hope that we don't have to do this, although I'd be willing to modify the central SConscript to optionally support hard-coded paths if there really is no alternative. > instead > of relying on an environment variable, which I am not allowed to set. All cctbx commands on PATH go through "dispatchers". To see how it works, look at any of the auto-generated scripts in the "bin" subdirectory of the build directory. The dispatchers are basically all the same; only the last few lines differ. Each dispatcher updates PYTHONPATH and DYLD_LIBRARY_PATH "just in time" to finally start the target command. I.e. there are no permanent settings in the environment. You just have to add the "bin" directory to PATH if you don't want to type the full path name to each command all the time (which will also work). Is this going to work for you? Cheers, Ralf

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differing build and install directories?
by William Scott 28 Sep '05

28 Sep '05

Dear Ralf: Sorry to keep pestering you. I'm now trying to build debian packages, which means the build directory differs from the install directory. Because of this, a lot of the shell scripts, python scripts, and compiled binaries in cctbx have a path like /sw/src/fink.build/ ccp4-5.99.3-1/ccp4-5.99.3 hard-coded into them, and I'd like the final one to look like /sw/share/xtal/ccp4-5.99.3 (for example). Similarly for Debian linux. Is there a simple way to build in one directory but use the final install-path for configuring? I've tried changing $install_root in the file cctbx_install_script.csh, but that didn't work. Similarly, I noticed the install_paths hard-coded into the dynamic libraries for cctbx are relative, rather than absolute like the others, for examle: % otool -L cctbx_dmtbx_ext.so cctbx_dmtbx_ext.so: /System/Library/Frameworks/Python.framework/Versions/2.3/ Python (compatibility version 2.3.0, current version 2.3.5) lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.0.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) Is there a simple way to change that? All the best, Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA

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Testing.....
by Erik Mckee 27 Sep '05

27 Sep '05

Hello :) Does this work? I'm surprised there aren't any test messages in the archives before now.... However, perhaps I'm just talking to myself here..... *Tests for echo.....

2 1