February 2017 - phenixbb - phenix-online.org

Cannot compile rosetta interface Centos 7 with 1.11.1
by ludovic Pecqueur 21 Apr '17

21 Apr '17

Dear Phenix developers, I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602 When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors). When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors. If you have any idea of the change between the two versions leading to this issue. Thank you for your help, Ludovic. ######################## Error message: Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source ~> phenix.python scons.py bin mode=release extras=python -j 8 scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

9 9

difference map for cryo-EM (cryo-EM map minus model map)
by Pavel Afonine 16 Mar '17

16 Mar '17

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

2 5

Open Postdoctoral Position at Oak Ridge National Laboratory
by Paul Adams 10 Mar '17

10 Mar '17

Dear Colleagues, on behalf of my colleagues I’d like to bring to your attention an open postdoctoral associate position at Oak Ridge National Laboratory (ORNL): Summary - To maximize the information obtained for diffraction experiments for structural biology, data processing methods need to be improved for marginal, weak data and also for reflection overlap. Methods will be developed that make use of knowledge about the atomic model to inform data processing methods so that reflections can be successfully deconvolved. A novel technique for full profile single crystal structure refinement will be developed. This work will be performed through a National Institutes of Health (NIH) funded consortium between ORNL and Lawrence Berkeley National Laboratory (LBNL) to develop a broad range of computational tools for macromolecular neutron crystallography. The aim of this consortium is to address the need for new computational tools and methods to deal with the increasing number of neutron macromolecular structures being determined and their increasing size and complexity. These tools will be developed in close collaboration with the PHENIX program, a NIH funded consortium between several groups. Interested candidates should visit: https://www.ornl.gov/careers Job Posting: Postdoctoral Research Associate - Computational Methods for Integrating Protein Crystallography Data / NB50615195 https://recruiting-internal.ornl.gov/sap/bc/erecruiting/posting_apply?param… -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

2 1

Phenix.refine ignores ligand planarity restraint
by Maike Bublitz 28 Feb '17

28 Feb '17

Dear all, this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine: I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in my indole group, although all respective atoms are included in the plane definition. At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand. How can I convince Phenix to not distort my ligand's aromatic rings? Many thanks for your kind suggestions. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 lab: +44 (0)1865 613318 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

8 13

estimated coordinate error from phenix.refine
by Almudena Ponce Salvatierra 28 Feb '17

28 Feb '17

Dear all, I would like to know how the estimated coordinate error is calculated in phenix.refine, the one that is written on the pdb file as "ML based". I'm asking due to the following: For example if I am comparing two different models (structures determined at 2.1 and 2 Angstroms) but one does have a coordinate error estimate of 0.25 Angstroms and the other one of 0.6, respectively. Is the first model more reliable? The second one is reliable too but my question points towards how conservative or how more conservative should I be when describing distances , potential H bonds, coordination. Despite those different numbers in estimated coordinate error, the electron density maps look very similar or almost the same for both structures, very clear and complete at 2 Angstroms. That's why I was somehow surprised to find these difference. Thank you very much in advance Best Almudena -- Dr. Almudena Ponce-Salvatierra EMBL-European Molecular Biology Laboratory 71, avenue des Martyrs - CS 90181 F - 38042 Grenoble Cedex 9

3 2

"RosettaScripts executable could not be located" error
by Yonglin Hu 24 Feb '17

24 Feb '17

Hello List, I have installed the rosetta (version 2016.32.58837) and phenix (dev-2689). I have no problem running phenix.mr_rosetta, but when I run phenix.rosetta_refine or rosetta.run_tests, I always get the following error message: Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. But I do have relevant environmental variables set up: ROSETTA3_DB=/usr/local/rosetta_src_2016.32.58837_bundle/main/database PHENIX=/usr/local/phenix-dev-2689 PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2016.32.58837_bundle PHENIX_VERSION=dev-2689 I would appreciate it if you could tell me what really went wrong. Have a nice day, Yonglin Hu

2 1

Phenix rosetta refine error
by pravin.jagtap＠embl.de 23 Feb '17

23 Feb '17

Hi All, I want to do phenix.rosetta refinement. I was successful in compiling rosetta and build the rosetta_refine interface. However when I try to do the refinement, I get the following error. I get the similar error in Rosetta_MR. Please let me know if you need any other information. Thanks and regards, Pravin. RuntimeError : Aborted due to error in job 1. Traceback: File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run return_value = self.target() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__ result = self.run() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 302, in run return run(args=list(self.args)) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 397, in run_jobs check_result(result) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) Platform info: __FILE__ = /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 18 2017 __TIME__ = 00:45:46 __TIMESTAMP__ = Tue Nov 8 23:38:16 2016 __x86_64__ __linux __GNUC__ = 4 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 7 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-16) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_55 PY_VERSION = 2.7.8 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 _OPENMP = 200805 gnu libc version: 2.17 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: 86799 os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-3.10.0-514.6.1.el7.x86_64-x86_64-with-centos-7.3.1611-Core platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 8,292,691,968 Memory free: 703,213,568 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', 'x00', 'e', 'x00', 'l', 'x00', 'l', 'x00', 'o', 'x00'] u"u00C5" = ['xc5', 'x00'] as utf-8 = ['xc3', 'x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

2 1

eBIC and CCP-EM Spring Symposia
by Tom Burnley 21 Feb '17

21 Feb '17

Dear all, eBIC and CCP-EM are proud to announce the inaugural symposium of eBIC, the UK national cryoEM centre at Diamond Light Source, and the third CCP-EM Spring Symposium on April 24–26, 2017. This three day conference will be held at the Diamond/RAL Campus, Harwell, Oxfordshire. The eBIC opening symposium will be on the first day, highlighting the advances of cryoEM and feature presentations with an emphasis on emerging and challenging technologies, followed by CCP-EM featuring of state-of-the-art presentations related to cryo-EM methods and applications. Confirmed speakers include: eBIC Speakers: Yifan Cheng, UCSF School of Medicine John Briggs, MRC Laboratory of Molecular Biology Lori Passmore, MRC Laboratory of Molecular Biology Radostin Danev Max Planck Institute of Biochemistry Greg McMullan, MRC Laboratory of Molecular Biology Sharon Wolf, Weizmann Institute of Science CCP-EM Speakers: Piet Gros, Utrecht University Maya Topf, Birkbeck / UCL David Waterman, STFC Tanmay Bharat, MRC Laboratory of Molecular Biology / University of Oxford Paul Adams, Lawrence Berkeley National Laboratory Tristan Croll, University of Cambridge Erik Lindahl, SciLifeLab Kay Grunewald, STRUBI Carolyn Moores, Birkbeck / UCL Morgan Beeby, Imperial College London Rob Nicholls, MRC Laboratory of Molecular Biology Ausra Domanska, University of Helsinki Becky Thompson, University of Leeds Full details and registration for the conference is provided here: http://www.ccpem.ac.uk/training/spring_symposium_2017/spring_symposium.php http://www.diamond.ac.uk/Home/Events/2017/eBIC-CCP-EM-Symposium.html Places are limited and registration will be on a first come first serve basis. We look forward to seeing you in April, Peijun, Tom & Colin and the rest of the eBIC and CCP-EM teams http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html http://www.ccpem.ac.uk/ -- Dr Tom Burnley, PhD CCP-EM | @ccp_em | www.ccpem.ac.uk Science and Technology Facilities Council (STFC) The Research Complex At Harwell Rutherford Appleton Laboratory, R92 OX11 0FA 01235 56 7871

1 0

Phenix User Meeting
by Nigel Moriarty 16 Feb '17

16 Feb '17

Folks Registration is open for Phenix User Meeting to be held Thursday 16th March 2017 at Lawrence Berkeley Lab. Following a morning of seminars about various areas of structure determine there will be tutorials for hands-on instruction of the Phenix programs. Participants should register below and forward any areas of particular interest to me. Also note that site access needs to be arranged for lab guests. Below is the link to the registration site for the Phenix Local Users Meeting. Please click on the following link: http://www.cvent.com/eve nts/phenix-local-users-meeting/event-summary-4c673041c511423 5b769d6af0d43db74.aspx Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Phaser multiprocessing with OpenMP available
by R.D. Oeffner 16 Feb '17

16 Feb '17

Hi all, On the Windows and the Linux Centos6 build we have recently enabled OpenMP of Phaser in Phenix as to take advantage of PCs with multiple CPUs. Feel free to try out these nightly builds and let us know about any problems. Regards, Robert -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html [1] Links: ------ [1] http://www.cimr.cam.ac.uk/investigators/read/index.html

1 0

changing mtz from P 31 2 1 to P 32 2 1
by Sebastiano Pasqualato 16 Feb '17

16 Feb '17

Hi guys, is there an utility in phenix to change hand of an mtz file? I’m interested in getting a P 32 2 1 mtz from a P 31 2 1. phenix.refine does handle the refinement in P 32 2 1 even with the P 31 2 1 mtz, but the polder map calculating tools complains about discrepancy between the pdb and the mtz. Thanks in advance, ciao, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit <http://is.gd/IEOXtalUnit>

2 1

Travel to ACA Meeting New Orleans May 26-30 2017
by Terwilliger, Thomas Charles 10 Feb '17

10 Feb '17

Colleagues, Like many of you, we are concerned over the recent upheaval surrounding travel to and from the United States.The ACA is committed to hosting an annual meeting that brings together a diverse community of scientists, no matter what their country of origin. Our mission includes diversity and a desire to foster a global community of structural scientists, in accordance with the principles of the International Union of Crystallography. While we understand any reluctance to travel to the US at this time, we would like to encourage anyone who is interested in attending the meeting in New Orleans this May to register now and to submit an abstract should you wish to present your work. We will offer a full refund of registration costs to anyone who is denied entry into the US or cannot risk the travel because of travel restrictions. We want you to know that all scientists are welcome at the ACA. Sincerely, The Members of the ACA Council Amy Sarjeant, President Tom Terwilliger, Past President Lisa Keefe, Vice President Sue Byram, Treasurer Diana Tomchick, Secretary Tomislav Friscic, Canadian Representative Hanna Dabkowska, IUCr Representative Bill Duax, CEO Marcia Colquhoun, Director of Admin. Services Kristina Vitale, Membership Secretary Please visit our website to learn more about the 2017 ACA Meeting http://www.amercrystalassn.org/2017-meeting-homepage

1 0

Job vacancy University of Manchester (3 positions)
by Colin Levy 10 Feb '17

10 Feb '17

Dear All, Please see below for details of several positions currently being advertised here at the University of Manchester. Many thanks, Colin Research Associate, Structural Biology / Enzymology (3 posts) Closing Date : 13/03/2017 Employment Type : Fixed Term Duration : 2 x 35 months plus 1 x 15 months Faculty / Organisational Unit : Science & Engineering School/Directorate : School of Chemistry Division : Chemical Biology & Biological Chemistry Hours Per week : Full-time Salary : £31,076 to £38,183 per annum Location : Manchester Institute of Biotechnology (MIB) Job Reference : S&E-09634 You will be working on Biotechnology and Biological Sciences Research Council (BBSRC)-funded projects in the group of Professor David Leys at the Manchester Institute of Biotechnology (MIB). These projects focus on structure-function relationship studies and biotechnological application of novel enzymes, and require individuals with a suitable background in structural biology and/or enzymology. You will join a large team of researchers in the Molecular Enzymology group at the MIB, and will receive training in a range of techniques as applied to establishing the structural and functional properties of the target enzymes. All posts are available with immediate effect, posts one and two ending 31 March 2020 and post three ending 31 May 2018. The School of Chemistry is strongly committed to promoting equality and diversity, including the Athena SWAN Charter for gender equality in higher education. The School holds a Silver Award which recognises their good practice in relation to gender; including flexible working arrangements, family-friendly policies, and support to allow staff to achieve a good work-life balance. We particularly welcome applications from women for this post. Appointments will always be made on merit. For further information, please visit http://www.chemistry.manchester.ac.uk/about-us/athena-swan/ Please note that we are unable to respond to enquiries, accept CVs or applications from recruitment agencies. Enquiries about the vacancy, shortlisting and interviews: Professor David Leys Email: david.leys(a)manchester.ac.uk<mailto:[email protected]> General enquiries: Email: hrservices(a)manchester.ac.uk<mailto:[email protected]> Telephone: 0161 275 4499 Technical support: Email: universityofmanchester(a)helpmeapply.co.uk<mailto:[email protected]> Telephone: 01565 818 234 Date of external posting: Thursday, 9 February 2017 This vacancy will close for applications at midnight on the closing date. [cid:[email protected]] Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN

1 0

solvent masks
by Kajander, Tommi A 10 Feb '17

10 Feb '17

Hi All, Was there a convenient way to make a solvent mask for a region with a model - its been a while - and use that to generate maps (i have a domain that is only partially visible, could not be found be molecular replacement), its there though. Could be that its not well ordered, but I was wondering if the bulk solvent masking is just wiping it out. (basicly something like half a domain, e.g. half of individual beta-strands, are missing.) resolution is bit limited (at best 3 Å) so automated building and refinement doesnt work terribly well. I could just place a model there and make a mask somewhere and include in map calculation? Thanks for suggestions, tommi

1 0

phenix.composite_omit_map
by Dyda 09 Feb '17

09 Feb '17

Dear Phenix BB, I have a moderate resolution structure that I refined using secondary structure restraints (both for nucleic acid and for protein) I'd like to use phenix.composite_omit_map to calculate such a map. Is it possible (and if so how) to make phenix.composite_omit_map to use the same restraints during annealing of the not omitted parts? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

2 1

Re: [phenixbb] Running Phenix Gui on Debian 8
by Chow, Martin 08 Feb '17

08 Feb '17

I am having troubling running Phenix 1.11.1.2575 gui under Debian 8 (Jessie), and have same results with different computers that are running the same system. I have no problem with previous versions like 1.9 and 1.10. However, with 1.11, Phenix guy won’t run. It complains about Gtk+ or Glib etc and quits. I know these are related to gui tool kits. I have tried Centro5, Centro6, and even compiled it, they all give similar or same complaints. I believe command-line works, but never try. However, simple commands like —version or —-help etc work. I just tried it on Red Hat, 1.11 works without issues. Clearly, it is a problem with the Linux Distro. Thank you. Martin Chow, Ph.D. Biochemistry University of Kentucky ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of phenixbb-request(a)phenix-online.org [phenixbb-request(a)phenix-online.org] Sent: Tuesday, February 07, 2017 3:20 PM To: phenixbb(a)phenix-online.org Subject: phenixbb Digest, Vol 135, Issue 4 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Computational Crystallography Newsletter, Volume 8, Number 1 (Nigel Moriarty) 2. Re: Phenix installation on manjaro (Murpholino Peligro) 3. Re: Phenix installation on manjaro (Billy Poon) 4. Re: Phenix installation on manjaro (Murpholino Peligro) 5. Re: Phenix installation on manjaro (Murpholino Peligro) 6. pdbtools atom_selection behavior (wtempel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Feb 2017 13:21:05 -0800 From: Nigel Moriarty <nwmoriarty(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org>, ccp4bb <CCP4BB(a)jiscmail.ac.uk>, developers(a)phenix-online.org, industry(a)phenix-online.org Subject: [phenixbb] Computational Crystallography Newsletter, Volume 8, Number 1 Message-ID: <CANkP=2eK6S4MWS=UJ=wZLXfC5qR9vQpgZEyi91gVv47EvdWQjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 ? O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

pdbtools atom_selection behavior
by wtempel 07 Feb '17

07 Feb '17

Hello all, suppose I would like to remove one alternate conformation B from residue 1 in chain A and set the occupancy of remaining atoms in that residue to 1. phenix.pdbtools alts_minim.pdb occupancies.set=1 \ occupancies.atom_selection=”chain A and resid 1” \ keep=”not (chain A and altid B and resid 1)” \ output.file_name=alts.out.pdb There are better methods to achieve that, but I eventually would like to expand this command to do other “things” to my coordinates. Well, so far I have failed to have the atom_selection to work the way *I* expect. stdout reveals that the program fails to apply a common scope to the command switches, and proceeds to reset occupancies of all atoms. Can this be done on the command line? A minimal (not) working example is attached, and your feedback appreciated. Best regards. Wolfram Tempel

2 1

Phenix installation on manjaro
by Murpholino Peligro 07 Feb '17

07 Feb '17

Dear all. has anyone been lucky with the installation of phenix in manjaro or any other archlinux-based distribution? Thanks Ps. Error looks like http://pastebin.com/WzwrbK8W

2 5

Computational Crystallography Newsletter, Volume 8, Number 1
by Nigel Moriarty 06 Feb '17

06 Feb '17

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Scale and merge multiple data sets
by Sam Tang 05 Feb '17

05 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

4 5

protein atom selection
by wtempel 03 Feb '17

03 Feb '17

Hello all, in my hands and to my surprise, PHENIX atom selections such as "protein" or "peptide" would include a co-factor like SAM. Did others notice that also? Is this behavior what most users would want or even expect? Best regards. Wolfram Tempel

4 5

Refine a structure with a disconnected region
by Yasser Almeida Hernández 02 Feb '17

02 Feb '17

Hi all, I am refining a structure at 1.9A, which contains a 7 residues C-terminal region. The resolution of the map in that region is low but is clear enough to define some side chains and the backbone. I build this region manually in Coot. This region is disconnected from the core of the protein, since the connecting loop cannot be seen in the density map. After running phenix.refine (GUI) and playing with the options several times, the final model of this region is always out of the map, even when the R values are improved. How can I refine the structure, keeping that part of the protein in its place, fitted to the map? Thanks in advance Best Yasser

2 1

10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 01 Feb '17

01 Feb '17

Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: beamline training; data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors, respectively; and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting of the technical difficulties the participants face in their projects. We have had considerable success resolving these problems in past years, attested by resulting publications http://www.ccp4.ac.uk/schools/APS-school/publications.php Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Registration fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

Announcement: Phenix tutorial videos
by Dorothee Liebschner 01 Feb '17

01 Feb '17

Dear Phenix users, Video tutorials about Phenix tools are now available on the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>. The videos give a short introduction about a Phenix tool, summarize the required input files and parameters, explain how to run it and – when appropriate – discuss the results. So far, the following topics are covered: - How to run phenix.refine - How to calculate polder maps - How to run phenix.real_space_refine - How to run PDB tools - How to change phenix.refine parameters via the GUI More videos will be added in the future. Feedback about the videos is very welcome (tutorials(a)phenix-online.org - or use the comment section on YouTube). If you are eager to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us: tutorials(a)phenix-online.org. Also, if you want to make your own Phenix tutorial and publish it on the channel, get in touch with us. Further info: To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to the channel to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button (next to the "subscribe" button). Best wishes, The Phenix team

1 0