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Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble
by Stephen Cusack 05 Mar '19

05 Mar '19

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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Are TLS parameters applied when TLS refinement is OFF?
by Mark Saper 04 Mar '19

04 Mar '19

I have a structure where at one stage TLS parameters were determined and then refined. It caused the R-free to increase so I stopped refining the TLS parameters. Are the TLS parameters still applied to the structure on subsequent refinement runs even when the TLS refinement is off? Is it appropriate to refine anisotropic B’s for a high resolution (1.35 Å) structure AND apply TLS parameters? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353 mobile: (734) 276-6505

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MAD merged dataset deposition
by Eugene Osipov 03 Mar '19

03 Mar '19

Hello, everyone, I have solved the structure of heme containing protein using anomalous signal from Fe atom (~1.739 anstroms) and further refined it using native dataset (0.9 angstroms). Structure was solved in AutoSol. The question is "What is the best way to deposit mtz with both datasets?" Should I merge and scale them simultaneously or can I deposit output file from AutoSol overall_best_refine_data.mtz, which contains F,FP, Rfree and HL coefficients? P.S.: please, respond in PM, I have only digest subscription on phenixBB. Thank you in advance! -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

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Rotamer restraints in phenix.real_space_refine
by Ashley Pike 28 Feb '19

28 Feb '19

Hi - Am I right in thinking that rotamer restraints behaves differently in latest official release (1.14-3260) compared to last but one official release (1.13-2998)? Issuing rotamer_restraints=True from command line or GUI used to give 0% rotamer outliers in the molprobity analysis at end of log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is as if they are not being applied. In the old log file it used to clearly print - **Update rotamer restraints*** after every macrocycle, in the 1.14 logs this is omitted. Many thanks, Ashley

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molprobity in phenix 1.14
by Roberto Marabini 25 Feb '19

25 Feb '19

Hi, In the past (phenix 1.13) I have been able to execute molprobity with the command line: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc d_min=2.200000 pickle=True pdb_interpretation.clash_guard.nonbonded_distance_threshold=None nproc=4 pdb_interpretation.clash_guard.nonbonded_distance_threshold=None ================== Unfortunately, for version 1.14 I get the error: ========================== Traceback (most recent call last): File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run map_params=params) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__ molprobity_map_params=map_params.input.maps) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__ from mmtbx.command_line.map_model_cc import get_fsc ImportError: No module named map_model_cc ============== That is, there is an error in the line "from mmtbx.command_line.map_model_cc import get_fsc" By the way, if I just run the command: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif ================== the program is executed without any problem. What should I do in order to execute molprobity.py with the option map_file_name. best wishes Roberto

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real space refine generates non-compliant PDB files
by Edwin Pozharski 22 Feb '19

22 Feb '19

Not sure whether anyone would care now that we got our marching orders to abandon PDB format and move to mmCIF, but the output of phenix.real_space_refine includes a number of lines that are not legit PDB records, i.e. this section ... REMARK 3 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.049 74053 ANGLE : 0.747 12.299 100513 CHIRALITY : 0.052 0.232 11312 PLANARITY : 0.006 0.069 13125 DIHEDRAL : 11.589 179.958 44947 MIN NONBONDED DISTANCE : 2.276 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.04 RAMACHANDRAN PLOT: OUTLIERS : 0.30 % ALLOWED : 8.63 % FAVORED : 91.06 % ROTAMER OUTLIERS : 8.76 % CBETA DEVIATIONS : 0 PEPTIDE PLANE: CIS-PROLINE : 3.7037037037 CIS-GENERAL : 0.0 TWISTED PROLINE : 1.85185185185 TWISTED GENERAL : 0.316455696203 REMARK 3 ... This does result in errors when this output PDB file is used as input to other software that is more stringent with format compliance. Cheers, Ed.

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Junior group leader opportunity in infection research (Braunschweig, Germany)
by Blankenfeldt, Wulf 22 Feb '19

22 Feb '19

Dear colleagues, I'd like to bring your attention to a job opening for a junior research group leader at the Helmholtz Centre for Infection Research in Braunschweig, Germany. The opening is broadly for infection research, and structural biologists should also feel encouraged to apply. The HZI has state-of-the-art facilities for x-ray crystallography and, through our participation in the CSSB on the DESY campus in Hamburg, to cryo-EM. We also have a protein sample production facility and equipment for biochemical/biophysical characterization. More details about the position and application requirements (deadline Feb. 28th!) can be found here: https://www.nature.com/naturecareers/job?id=672825 Best regards, Wulf ________________________________ Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig R?diger Eichel, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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run phenix.refine in command line error
by 张士军 18 Feb '19

18 Feb '19

Dear I cannot run the *.params file when I use command line to run phenix.refine. Does have any default *.params file format, which I can edit it according to my case? Can you sent me one if does exist? Thanks . Best regards Shijun

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error installation dev-1.14.3405 - 1.14.3409
by Guenter Fritz 13 Feb '19

13 Feb '19

Dear phenix developers, I get errors trying to install latest builds from 1.14.3405, 3406, 3409 64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem. The downloaded file is OK. 1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem. I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally? Best regards, Guenter Output trying to install from source: [guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse Similar from an installer: [guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

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CryoEM post-doctoral position
by Hasan, Syed Saif 07 Feb '19

07 Feb '19

A post-doctoral research position is high-resolution single particle cryoEM is available immediately in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple projects in structural biology of membrane protein complexes involved in cancer and viral pathogenesis. The researcher will have independence to guide the direction of their research and to pursue novel ideas should they find an interesting scientific question related to the general focus of my laboratory. IBBR is home to a large community of structural biologists. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Gatan K3 direct electron detector. A 200keV Thermo Fisher Glacios microscope equipped with a Falcon III direct electron detector will be acquired soon. A 120 keV FEI Tecnai T12 TEM equipped with a CCD camera is available for negative stain imaging. In addition to the latest cryoEM facilities, IBBR offers access to tools in X-ray crystallography, NMR, small angle X-ray scattering, mass-spectrometry and computational biology, and provides opportunities to work closely in collaboration with scientists in industry and in national labs located nearby (i.e., NIH, NIST). Applicants should have experience in sample preparation, data collection and data processing for single particle cryoEM. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and up to 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology University of Maryland School of Medicine 108 N. Greene St., Baltimore, MD 21201 Institute for Bioscience and BiotechnologyResearch (IBBR) 9600 Gudelsky Drive, Rockville, MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan

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