- cctbxbb - phenix-online.org

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

15 Dec '10

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

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

14 Dec '10

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

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

24 Nov '10

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

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

23 Nov '10

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

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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 16 Nov '10

16 Nov '10

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

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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 04 Nov '09

04 Nov '09

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

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

02 Nov '09

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

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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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