- phenixbb - phenix-online.org

real space rotamer restrains
by Leonid Sazanov 22 Jan '21

22 Jan '21

Hi, Is there somewhere a description of all the new parameters in phenix.real_space_refine rotamer restrains? I mean rotamers { fit = all *outliers_or_poormap outliers_and_poormap outliers poormap restraints { enabled = True sigma = Auto target = max_distant min_distant exact_match fix_outliers } tuneup = outliers outliers_and_poormap } What is poormap? What is the range of Sigma? What are those types of target? With the latest nightly build, with default parameters starting model with 1% of rotamer outliers ends up with 10% (not using local_search, as it was done before). To minimise number of outliers, which parameters can be changed? Lower Sigma? Switch on tuneup? Thanks for any info! Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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phenix.ligandfit, specifiy already generated cif file
by Guenter Fritz 22 Jan '21

22 Jan '21

Dear all, I would like to run phenix.ligandfit with a cif file I have already generated with acedrg or grade. This is not really required, just for comparison reasons. Would be nice. There is the parameter cif_already_generated= False / True But how do I define the cif file? Many thanks and best regards! Guenter

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Call for Abstracts: Michael G. Rossmann Memorial Symposium at the Microscopy & Microanalysis 2021
by Hasan, Syed Saif 20 Jan '21

20 Jan '21

Dear Colleagues, We cordially invite you to the “Michael G. Rossmann Memorial Symposium” at the Microscopy & Microanalysis 2021 conference, to be held in Pittsburgh, PA, Aug 1-5, 2021. This symposium focuses on the application of hybrid methods in electron microscopy of viruses, enzymes and other macromolecules, areas in which Michael was a pioneer. The symposium will feature invited talks from Prof. Hao Wu (Harvard Medical School), Prof. Rui Zhao (University of Colorado School of Medicine), and Prof. Chuan (River) Xiao (University of Texas El Paso). We invite abstracts from speakers in academics and industry at all career levels who develop and apply cutting-edge structural biology approaches to the study of viruses, viral proteins, enzymes, membrane proteins, and other systems. Ten abstracts will be selected for 15-minute oral presentations whereas the remaining abstracts will have the opportunity to be selected for poster presentations. Please note that the deadline for abstract submission is February 18, 2021. You will have the opportunity to select your preference for either in-person or virtual presentation. For additional meeting information and to register and submit your abstract, visit: https://www.microscopy.org/MandM/2021/ Deadline for abstract submission: February 18, 2021 We look forward to hosting you and learning about your exciting science at the M&M 2021 meeting. Sincerely, Terje Dokland (University of Alabama at Birmingham, Birmingham AL) S. Saif Hasan (University of Maryland School of Medicine, Baltimore MD)

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Retaining hydrogen in ligand while carrying out automatic ligand fitting.
by Rangarajan Erumbi 19 Jan '21

19 Jan '21

Hi, I am using phenix.ligandfit to automatically fit a ligand in to the ligand site of a protein model using the experimentally derived structure factors for the complex. The ligand pdb and restraints are created using phenix.elbow which contains the hydrogen atoms. However, after phenix.ligandfit the coordinates that are derived is stripped of all the ligand hydrogens. I want to retain the hydrogens only on the ligand during the refinement to preserve the overall geometry of the ligand. I am trying to do this automatically over several datasets with different ligands. I don’t see any specific parameter in the phenix.ligandfit that would specifically allow me to retain the ligand hydrogens. Phenix.reduce or phenix.ready_set does add hydrogens to entire coordinates including protein residues and so could not use it directly. Is there a way to get this accomplished in a simple way? Thanks in advance and appreciate your suggestions. Rangarajan.

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postdoc position, automated ligand placement
by Gabor Bunkoczi 17 Jan '21

17 Jan '21

Dear All, We have an opening for skilled post-doctoral researcher with an interest in software development at our Cambridge (UK) site. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-ad… Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

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PhD position available
by Tobias Beck 14 Jan '21

14 Jan '21

Dear all, We have an opening for a PhD position in my group. The Beck group is located at the University of Hamburg, with labs well-equipped for nano chemistry and protein chemistry. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. The project will focus on the design and synthesis of novel biohybrid nanostructures based on proteins and anisotropic inorganic nanoparticles. The post is part of the interdisciplinary research consortium 'Nanohybrid' and is available starting on April 1st 2021. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/… Link to the group homepage: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html Link to the research consortium 'Nanohybrid' webpage: https://www.chemie.uni-hamburg.de/en/forschung/grk-nanohybrid/ Deadline for applications is Feb 15 2021. I'd appreciate it if you could pass this announcement on to potentially interested candidates. Please contact me for further information or informal inquiries: tobias.beck @chemie.uni-hamburg.de Best, Tobias. ____________________________________________________________ Prof. Dr. Tobias Beck University of Hamburg Department of Chemistry Institute of Physical Chemistry Grindelallee 117 D-20146 Hamburg Germany phone: +49 4042838 8210 fax: +49 4042838 3462 web: www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/ ____________________________________________________________

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Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 14 Jan '21

14 Jan '21

Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. (https://tinyurl.com/MBGpostdoc) We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

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Phenix version 1.19 released
by Paul Adams 11 Jan '21

11 Jan '21

The Phenix developers are pleased to announce that version 1.19 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.19 version of Phenix: - phenix.real_space_refine: - Improved rotamer fitting (use multiprocessing, in case of NCS constraints work on one copy only and propagate changes to all related copies, various performance improvements and bug fixes) - Improved map/restraints weight calculation - Morphing can now use multiprocessing (nproc) - phenix.map_to_model and phenix.trace_and_build - Improved high-resolution model-building including detection of insertions and deletions - New methods - phenix.local_resolution: calculates a local resolution map - phenix.local_aniso_sharpen: optimizes a map taking into account local resolution-dependence and anisotropy of the map and its errors - New scripting tools - High-level scriptable Python tools are now available for map and model analyses and manipulation as well as for model-building - Restraints - Adjusting the "positions" of atom names in (pseudo-)symmetric amino acid side chains is now the default - Improved restraints for ARG allows more flexibility of the CD atom - Bug fixes - Chains with modified amino or nucleic acids can be aligned - Fixed handling of modified amino/nucleic acids in sequence alignment For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Post-doc vacancy in cryoem of viruses
by Hasan, Syed Saif 11 Jan '21

11 Jan '21

Dear Colleagues, A vacancy for a post-doctoral researcher is available immediately in my lab in the University of Maryland Center for Biomolecular Therapeutics located on the campus of Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ibbr.…>) in Rockville MD. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses utilize structural similarities with host proteins to hijack inter-organelle communication. Prior experience in insect cell culture for recombinant protein production is desirable. Expertise in cryoEM or X-ray crystallography will be advantageous. Candidates who have recently completed their PhD are encouraged to apply. IBBR is located 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 kV Talos Arctica with a Falcon 3EC DED and a 200 kV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have a Vitrobot Mark IV and a Cp3 cryo-plunger for sample preparation. We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. Interested candidates should send their CV and a cover letter to me at sshasan(a)som.umaryland.edu ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Senior Technician Position at the Biochemistry and Structural Biology Unit - IEO Milano
by Sebastiano Pasqualato 11 Jan '21

11 Jan '21

Dear all, a position is open at the Biochemistry and Structural Biology Unit of the European Institute of Oncology in Milan. The Unit (https://www.research.ieo.it/research-and-technology/technological-units/bio… <https://www.research.ieo.it/research-and-technology/technological-units/bio…>) is one of the technological platforms of the Department of Experimental Oncology of the European Institute of Oncology (www.research.ieo.it <http://www.ieo0researh.it/>), a comprehensive cancer centre located in the south area of Milan. We provide services and support to the department in the fields of Biochemistry and Structural Biology and collaborate both with scientific groups of the department and external ones to foster the structural biology aspects of their projects. The ideal candidate has a Master/PhD degree in Chemistry, Biotechnology or Biology, with strong interest in biochemistry and structural biology. We are looking for an enthusiastic, motivated person, with good organisational and relational skills, and a good knowledge of English. She/he will take care of assisting scientists collaborating with the Unit in macromolecular samples purification, characterisation and crystallisation, managing sample shipment to synchrotrons, supervising instrumentation usage and maintenance. The Unit is setting up a Cryo-EM lab with an in-house VitroBot blotting device and external Electron Microscopy access, which the candidate is expected to manage. Experience in setting up grids and Cryo-EM data collection will be a distinguishing skill. Potential applicants are encouraged to contact Dr. Sebastiano Pasqualato, sending a brief description of interests, and a CV with at least one referee contact to sebastiano.pasqualato(a)ieo.it <mailto:[email protected]>. Best regards, Sebastiano -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology 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: https://www.research.ieo.it/research-and-technology/technological-units/bio…

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