- cctbxbb - phenix-online.org

FW: Problems with cctbx - Explore symmetry
by robert.mcmeeking＠stfc.ac.uk 19 Feb '16

19 Feb '16

Dear Colleagues I may not have sent my previous message to the most appropriate email address. I now forward including the "phenix-online.org" one. Is there anyone out there who can point me in the right direction? Best Regards Bob From: McMeeking, Robert (STFC,DL,SC) Sent: 13 February 2016 12:18 To: cctbx(a)cci.lbl.gov Cc: McMeeking, Robert (STFC,DL,SC) Subject: Problems with cctbx - Explore symmetry Hello from the UK I am currently experiencing problems with the Explore symmetry web service - http://cci.lbl.gov/cctbx/explore_symmetry.html. When dealing with a particular Hall Symbol there is a cctbx runtime error (Malformed matrix symbol). The symbol in question is: -R 3 2"c It represents a setting for Space Group R -3 c :H (167) I am practically certain this worked fine in the past. I suspect the problem may be related to parsing the double quote symbol. If I replace with a single quote it manages to run OK, but the output information is a non-standard setting for Space Group 165. By way of background: I call the web service from my own CGI script and extract the symmetry operators that I need to display the crystal structure in question. The Hall symbol used is from the Crystallographic Open Database CIF (COD 2100992). I noticed the problem very recently, but because I cache information it is not clear when the problem first appeared. I only need to go through this process when explicit symmetry operators are not present in the CIF in question. I have not, as yet, installed the cctbx system on our server. Inoticed the problem when using our CrystalWorks system to attempt to display entries from the Crystallography365 Project http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17 Best Regards Bob Dr R.F. McMeeking Honorary Scientist STFC Chemical Database Service at Daresbury

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Updated base dependencies (not Boost)
by Billy Poon 19 Feb '16

19 Feb '16

Hi all, I have a set of new dependencies for base running on a CentOS 6.7 machine. The tests for PHENIX pass, but I'm still testing the GUI. It looks like most of the DIALS tests pass, but there are some that fail due to an updated Python Imaging Library. Testing will take a while longer, but I attached the modified install_base_packages.py and package_defs.py scripts for anyone who wants to try it out. Just use these in place of the ones in cctbx_project/libtbx/auto_build. I'll also clean up the scripts (e.g. remove cruft from the migration to wxPython 3.0.2, refactor some functions) once testing is complete. Aaron and I will be setting up "clean" virtual machine images for CentOS 5, 6, and 7, and Ubuntu 12.04, and 14.04, and eventually Windows 10 and maybe OS X (only Server can be virtualized) for testing the installers. The goal is to simulate what a user would get from a fresh install of an OS and test that our installers work correctly. And after each test, we can revert the virtual machine to an earlier snapshotted state. This should help in debugging some of the recent installation issues. Since our installers include the GUI, the Linux images will have their respective desktop GUIs installed (desktop version instead of server version). We thought about going with minimal server installs, but there are external dependencies, namely X11/Xorg, that we expect the users to have, and installing the desktop GUI would be the easiest way to satisfy any external dependency. Some highlights from the updates, 1) Python Imaging Library has not been updated since 2009. There is an active fork called Pillow that seems to be mostly backwards compatible. I have noticed one change in the API (replace PIL.Image.fromstring with PIL.Image.frombytes), but more testing is needed. 2) The updated version of ReportLab depends on Pillow. 3) GTK2 was not updated to GTK3 since it seems like wxPython only added support for GTK3 in 3.0.2. GTK2 is updated to the latest version. Dependencies for GTK2 (cairo, pango, etc.) are updated. An additional package, HarfBuzz, is needed. 4) libPNG was updated only to 1.5.x, not 1.6.x, because 1.6.x has some stricter checks on the image. Warnings are raised in the GUI. Eventually, this can be upgraded to 1.6.x, but I would need to reprocess all of the PNG icons to remove the offending bits. 5) libFFI was added for the updated version of glib. The updated dependencies have been built on CentOS 5, 6, and 7, and OS X 10.10, but not all the tests have been run yet. The 32-bit version of CentOS 5 is going to require some more work before the updated packages will compile. Let me know if there are any questions or suggestions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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mon_lib dependency
by Roger Martin 01 Feb '16

01 Feb '16

Hi, looking at the prebuilts(http://cci.lbl.gov/cctbx_build/dev-565/cctbx-installer-dev-565-in… for CentOS I see the dependency for mon_lib in verify_mon_lib_data.py. Is mon_lib available stand alone or comes in the full ccp4 package only? Where do most of you get a copy of mon_lib?

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FW: Mac builds currently broken on Jenkins
by markus.gerstel＠diamond.ac.uk 29 Jan '16

29 Jan '16

Sorry, this should have gone onto cctbx list. This is running bootstrap.py --builder=dials build on MacOS X, but I don't think it is specific to dials. -Markus From: Gerstel, Markus (DLSLtd,RAL,LSCI) Sent: 22 January 2016 08:51 To: dials-support(a)lists.sourceforge.net Subject: Mac builds currently broken on Jenkins During the build step this happens: (..) /usr/bin/c++ -o annlib_adaptbx/self_include/bd_fix_rad_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_fix_rad_search.cpp In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/ann/ann_adaptor.cpp:3: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include/annlib_adaptbx/ann_adaptor.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/flex_types.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/accessors/flex_grid.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small_plain.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny_plain.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/detail/misc.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/type_traits.h:29: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits.hpp:13: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/add_const.hpp:16: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/type_trait_def.hpp:14: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/template_arity_spec.hpp:10: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int_fwd.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/adl_barrier.hpp:17: /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/config/adl.hpp:17:10: fatal error: 'boost/mpl/aux_/config/msvc.hpp' file not found #include <boost/mpl/aux_/config/msvc.hpp> ^ /usr/bin/c++ -o annlib_adaptbx/self_include/bd_pr_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_pr_search.cpp /usr/bin/c++ -o annlib_adaptbx/self_include/bd_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_search.cpp In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/ann/boost_python/annlib_ext.cpp:2: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include/annlib_adaptbx/ann_adaptor.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/flex_types.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/accessors/flex_grid.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small_plain.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny_plain.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/detail/misc.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/type_traits.h:29: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits.hpp:13: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/add_const.hpp:16: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/type_trait_def.hpp:14: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/template_arity_spec.hpp:10: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int_fwd.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/adl_barrier.hpp:17: /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/config/adl.hpp:17:10: fatal error: 'boost/mpl/aux_/config/msvc.hpp' file not found #include <boost/mpl/aux_/config/msvc.hpp> ^ 1 error generated. scons: *** [annlib_adaptbx/ann/ann_adaptor.o] Error 1 1 error generated. scons: *** [annlib_adaptbx/ann/boost_python/annlib_ext.o] Error 1 scons: building terminated because of errors. usr+sys time: 3.36 seconds, ticks: 13399823, micro-seconds/tick: 0.251 wall clock time: 15.72 seconds Performing actions: build ===== Running in .: deleting dist, tests, tmp removing .pyc files in /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules removed 3 files ===== Running in build: run configure.py ===== Running in build: save configure command ===== Running in build: libtbx.scons Process failed with return code 2 Build step 'Execute shell' marked build as failure -Markus -- 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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dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

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Git (again)
by Graeme.Winter＠diamond.ac.uk 15 Jan '16

15 Jan '16

Hi Folks so, while this is tangential to the discussion of whether or not to move to git, I will observe that our chosen repo supplier appears to be taking some down time again: [gw56@ws133 format]$ svn commit -m "Comment about application of this format" Sending format/FormatSMVRigakuEiger1M.py Transmitting file data .svn: Commit failed (details follow): svn: Can't create directory '/svn/p/cctbx/code/db/transactions/23592-1.txn': Permission denied Over the last year this has not been such a rare occurrence and is always annoying when it does happen. The sourceforge.net website is temporarily in static offline mode. Only a very limited set of project pages are available until the main website returns to service. While this is I agree unrelated to the revision control we elect to use, it should perhaps be part of the same discussion. Meanwhile, all builds for dials will be gone until sf.net is once again live... awesome! Cheerio Graeme -- 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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Re: [cctbxbb] dials install error
by markus.gerstel＠diamond.ac.uk 13 Jan '16

13 Jan '16

Dear Sid, Unfortunately I don't know what the proper solution to your problem is. We had issues with pango/glibc reported just a few days ago, but I don't know what the outcome to that was. Dear David, Nick, Billy, Following up on the discussion in the thread 'bootstrap.py build on Ubuntu', here is an installer failure on CentOS5 that comes down to pango/libfontconfig/libglib missing some libraries, trace attached. -Markus From: Sidhu, Khushwant (Dr.) [mailto:[email protected]] Sent: 12 January 2016 11:26 To: Gerstel, Markus (DLSLtd,RAL,LSCI) Cc: Sidhu, Khushwant (Dr.) Subject: Re: dials install error Dear Markus, using the --verbose flag, I get the following .... ./install --verbose (snip) : Regenerating module files in /usr/local/dials-dev20160112/base : generating pangorc file at /usr/local/dials-dev20160112/base/etc/pango/pangorc : generating pango.modules file at /usr/local/dials-dev20160112/base/etc/pango/pango.modules : /usr/local/dials-dev20160112/base/bin/pango-querymodules: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /usr/local/dials-dev20160112/base/lib/libfontconfig.so.1) : /usr/local/dials-dev20160112/base/bin/pango-querymodules: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /usr/local/dials-dev20160112/base/lib/libglib-2.0.so.0) : Traceback (most recent call last): : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py", line 22, in <module> : if not run(): : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py", line 17, in run : libtbx.env_config.cold_start(sys.argv) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py", line 2267, in cold_start : env.refresh() : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py", line 1544, in refresh : regenerate_module_files.run(libtbx.env.under_base('.'), only_if_needed=True) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 153, in run : fix_pango(base_dir, out) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 59, in fix_pango : call(("%s/bin/pango-querymodules > %s") % (base_dir, pangomodules), log=out) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/installer_utils.py", line 81, in call : raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) : RuntimeError: Call to '/usr/local/dials-dev20160112/base/bin/pango-querymodules > /usr/local/dials-dev20160112/base/etc/pango/pango.modules' failed with exit code 1 Traceback (most recent call last): File "/usr/local/dials-installer-dev/bin/install.py", line 46, in ? installer(sys.argv[1:]).install() File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 318, in install_from_binary self.reconfigure(log=log) File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 484, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/dials-dev20160112/base/bin/python /usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/dials-dev20160112/build dials xia2' failed with exit code 1 regards Sid -- 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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status of mmtbx/phenix.molprobity
by Marcin Wojdyr 04 Jan '16

04 Jan '16

Dear All, we'd like to use mmtbx validation code. Is all the code in mmtbx meant to be open-source, even if the dispatchers have names starting with phenix? In particular I'm thinking about phenix.molprobity. (the names are not a problem, I just want to double check that it's ok if we use it) All the best in 2016, Marcin

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Failure in phenix.map_box when working with map files....
by Ezra Peisach 12 Dec '15

12 Dec '15

Has anyone observed a failure of phenix.map_box when working with map files? When working with a structure factor file with map coefficients, it works fine. When a map file is used - the following occurs: Traceback (most recent call last): File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 194, in <module> run(args=sys.argv[1:]) File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 158, in run selection = selection) File "/local/scratch/CCTBX/cctbx_sources/mmtbx/utils/__init__.py", line 2938, in __init__ self.map_box = maptbx.copy(map_data, gridding_first, gridding_last) Boost.Python.ArgumentError: Python argument types in cctbx_maptbx_ext.copy(double, list, list) did not match C++ signature: copy(scitbx::af::const_ref<double, cctbx::maptbx::c_grid_padded_p1<3ul> > map_unit_cell, scitbx::af::tiny<int, 3ul> first, scitbx::af::tiny<int, 3ul> last) copy(scitbx::af::const_ref<float, cctbx::maptbx::c_grid_padded_p1<3ul> > map_unit_cell, scitbx::af::tiny<int, 3ul> first, scitbx::af::tiny<int, 3ul> last) copy(scitbx::af::const_ref<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > map, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > result_grid) copy(scitbx::af::const_ref<float, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > map, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > result_grid) Any suggestions? The map_data is the same format in the call....

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crystallography Q&A site proposal on StackExchange
by Marcin Wojdyr 06 Nov '15

06 Nov '15

Hello, I'm writing about it first to developer mailing lists assuming that developers know StackOverflow. SO has now a number of sister sites on StackExchange and some Q&A sites in the same format are self-hosted, e.g. biostars.org. Here is a list of sites in the science category on SE: http://stackexchange.com/sites#science-traffic I though that such a site for crystallography would be useful, mostly because it has lower psychological and technical barrier for asking questions. I'm not sure how it's on phenixbb and other mailing lists, but on ccp4bb maybe a few percent of all 6000+ subscribers have asked anything at all. I assume people have questions in mind, they are just not eager to ask it by mailing 6000 other people. I don't know if a Q&A site would help, but just to try here is proposal for Crystallography site on SE: http://area51.stackexchange.com/proposals/91841/crystallography Using SE is simpler than hosting it, and even if the proposal doesn't make it at least we'll have an idea what was the interest. Technicalities. New sites are created basically when enough people is interested. Currently the proposal is in the "definition" stage, which means coming up with example questions - to show what kind of questions could be asked when the site exists. To complete this stage we need 40 question with 10+ votes. Everyone has 5 up-votes for selecting good questions. Votes can be changed at any time. So at least 80 voting people would be needed for this stage. Having more example questions would also help. Marcin

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