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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 25 Feb '17

25 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 24 Feb '17

24 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 17 Feb '17

17 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 17 Feb '17

17 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 11 Feb '17

11 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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