- phenixbb - phenix-online.org

phenix ensemble ref.
by Kajander, Tommi A 23 Mar '17

23 Mar '17

Hi, is it possible to do ensemble refinement in phenix with just one domain? (and e.g. fix the other) Doens seem so? Thanks, Tommi

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Re: [phenixbb] Error running phenix.rosetta_refine tests with Rosetta 3.8
by Nigel Moriarty 21 Mar '17

21 Mar '17

Oliver My Rosetta 3.7 is 2016.32. Not sure why we are different. 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 On Tue, Mar 21, 2017 at 8:19 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Nigel, > > I tried with rosetta 3.7 (2016.46) and phenix dev-2719, and this time > compilation using rosetta.build_phenix_interface was successful (scons > finished building targets with no errors), but when I run rosetta.run_tests > it still crashes, though with a different error (see attached log). Any > ideas as to how to fix? > > Cheers > Oli > > > > On Mar 20, 2017, at 7:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > Oliver > > We are currently only supporting up to Rosetta 3.7 as a c++11 compiler is > required for any subsequent versions. We have compiled using a c++11 > compiler with no problems so I suggest you revert to 3.7 or check the logs > for compilation problems. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 <(510)%20486-5709> Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov > <http://cci.lbl.gov/> > > On Mon, Mar 20, 2017 at 9:34 AM, Oliver Clarke <olibclarke(a)gmail.com> > wrote: > >> Hi, >> >> Phenix rosetta refinement worked with previous versions of rosetta and >> phenix, but with the latest Rosetta version (3.8) and latest phenix nightly >> I get a crash when running rosetta.run_tests after building the rosetta >> phenix interface, which runs a test run of phenix.rosetta_refine. It gets >> to the stage of generating initial models and then crashes - see attached >> log. Ideas for a fix welcome! >> >> Cheers >> Oli >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > >

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Error running phenix.rosetta_refine tests with Rosetta 3.8
by Oliver Clarke 21 Mar '17

21 Mar '17

Hi, Phenix rosetta refinement worked with previous versions of rosetta and phenix, but with the latest Rosetta version (3.8) and latest phenix nightly I get a crash when running rosetta.run_tests after building the rosetta phenix interface, which runs a test run of phenix.rosetta_refine. It gets to the stage of generating initial models and then crashes - see attached log. Ideas for a fix welcome! Cheers Oli

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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

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Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.
by Mooers, Blaine H.M. (HSC) 16 Mar '17

16 Mar '17

Hi Andy, Thank you for the clarification! Yes, I was wrong. There is still a tools subdirectory at the top level. I installed the latest version of Rosetta from source. This is version 3.8, the Feb. 25th, 2017 release. The rosetta\_options.py file is in the same location: main/source/src/apps/public/ERRASER. Following up on your suggestion, I edited the file erraser.py in /Applications/phenix-dev-2686/modules/phenix/phenix/erraser by replacing line 543 with the following: file_path = os.path.join(params.directories.rosetta_path, 'main/source/src/apps/public/ERRASER') Phenix.erraser now runs. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu ________________________________ From: Andy Watkins [andy.watkins2(a)gmail.com] Sent: Tuesday, March 14, 2017 11:53 AM To: Mooers, Blaine H.M. (HSC) Subject: Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH Yes, while the tools directory should still exist, the new path to ERRASER is in fact main/source/src/apps/public. I wonder if the issue lies in Phenix's subsequent interpretation of that environment variable -- i.e., the Phenix code is appending "tools/ERRASER" instead of the aforementioned path. On Mar 14, 2017 9:18 AM, "Mooers, Blaine H.M. (HSC)" <Blaine-Mooers(a)ouhsc.edu<mailto:[email protected]>> wrote: Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_depa…> X-ray lab (LBSF)<https://urldefense.proofpoint.com/v2/url?u=http-3A__http-3A__research.ouhsc…> Molecular Graphics<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Links <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Small Angle Scattering <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs…> office: (405) 271-8300<tel:(405)%20271-8300> lab: (405) 271-8313<tel:(405)%20271-8313> e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb<https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai…> Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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phenix.erraser and PHENIX_ROSETTA_PATH
by Mooers, Blaine H.M. (HSC) 14 Mar '17

14 Mar '17

Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu

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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 ] --

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Please attend a workshop on Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography
by Robert Sweet 08 Mar '17

08 Mar '17

Driven by recent advances in this field we will hold a workshop to discuss it. The workshop will be on Monday, May 15, 2017 at Brookhaven Nat'l Laboratory, and will be affiliated with the 2017 Users' Meeting for NSLS-II and the Center for Functional Nanomaterials. The current draft agenda is on-line here: http://usersmeeting.ps.bnl.gov/workshops/workshop.aspx?year=2017&id=136 Registration for the Workshop and Users' Meeting is here: http://usersmeeting.ps.bnl.gov/registration/?year=2017 A description of the workshop is below. The Organizers: Robert Sweet (NSLS-II, BNL), Michael Wall (LANL), Nozomi Ando (Princeton University), James S. Fraser (University of California, San Francisco), George N. Phillips, Jr. (Rice University) For answers to questions, please contact Wall: mewall(a)lanl.gov or Sweet: sweet(a)bnl.gov Description: X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins. A major focus of the workshop will be to provide a roadmap to the acquisition of reliable data by surveying measurement methods and discussing the increase in measurement accuracy enabled by improved detectors, experimental methods, and data integration. Missing from recent results is real information about the behavior of the molecules being studied that would guide the thinking of biochemists and biologists. To discuss these and their relative merits will be a second major focus of the workshop. The charge to this workshop will be to provide a roadmap to efforts that will provide the biological understanding we believe is hidden in the data. ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Deputy Director, LSBR: The Life Science and ^ (that's L Biomedical Technology Research Center at NSLS-II not 1) Photon Sciences and Biology Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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on tst_af_3.exe
by Smith Liu 08 Mar '17

08 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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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

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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

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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

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phenix.composite_omit_map
by Dyda 10 Feb '17

10 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

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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

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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

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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

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