- phenixbb - phenix-online.org

on tst_af_3.exe
by Smith Liu 07 Mar '17

07 Mar '17

Dear All, What is the function of tst_af_3.exe in Phenix? It was in category "array_family", and a antivirus software in my computer has killed it as trojan. Smith

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map_to_model space group symbol not recognized
by CPMAS Chen 06 Mar '17

06 Mar '17

Hi, All when I try to using map_to_model tool to optimize my model from low-resolution map, phenix.map_to_model refine_2.mtz seq_from_pdb.dat I got the following error, even though I did not provide ncs file, Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec Traceback (most recent call last): File "/usr/local/phenix-1.11-2567/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module> run(sys.argv[1:],out=sys.stdout) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run tracking_data=run_segment_and_split_map(params,out=out) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params params=get_params_from_args(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args return command_line.work.extract() File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/iotbx/phil.py", line 40, in from_words return sgtbx.space_group_info(symbol=str(symbol)) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__ symbols = space_group_symbols(symbol) RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20> Would this be a bug or I simply missed something? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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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>

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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

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"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

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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

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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

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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

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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

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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>

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