- phenixbb - phenix-online.org

(no subject)
by Smita Yadav 29 Jul '21

29 Jul '21

Hello all, Can someone suggest to me, how we can decide the resolution range in the outer shell during the protein crystal data set. And one more thing. processing into different Laue groups and point groups how much it will change the dataset. -- With Regards Smita Yadav

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Visiting Research Specialist Position | Polikanov Lab | University of Illinois at Chicago
by Yury Polikanov 27 Jul '21

27 Jul '21

The Polikanov Lab is seeking a Visiting Research Specialist. The successful candidate will conduct research by using X-ray crystallography techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. Expert-level knowledge of the programming languages (such as Python) is highly desirable. The successful candidate would conduct his own research and assist with the principal investigator’s research while training other laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties:* • Perform research relevant to the assigned projects; • Isolate and crystallize bacterial ribosomes; • Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; • Collect X-ray diffraction data from the ribosome crystals at the APS Synchrotron; • Perform data analysis; coordinate, analyze, and document results for publication; • Directly participate in writing papers and grants based on the experimental data; • Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; • Attend weekly group meetings and journal clubs. *Minimum qualifications:* • Bachelor’s degree in chemistry, biochemistry, biophysics, or a related field; • Master’s degree or higher is preferred; • Minimum 3 years of laboratory research experience; • Strong background in biochemistry and molecular biology; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is desired; • Experience in RNA biology is desired. • The successful candidate should be able to walk into the laboratory and be able to start working without significant additional training in basic molecular biology techniques. *For fullest consideration, interested candidates should submit an application, including CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=149023 <https://jobs.uic.edu/job-board/job-details?jobID=149023> by August 9, 2021. Questions can be directed to Dr. Polikanov at yuryp(a)uic.edu <yuryp(a)uic.edu>. **In the cover letter, describe what your scientific interests are and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* *The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer including Disability/Vets.* *Offers of employment by the University of Illinois may be subject to approval by the University’s Board of Trustees and are made contingent upon the candidate’s successful completion of any criminal background checks and other pre-employment assessments that may be required for the position being offered. Additional information regarding such pre-employment checks and assessments may be provided as applicable during the hiring process.* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit https://www.hr.uillinois.edu/cms/One.aspx <https://www.hr.uillinois.edu/cms/One.aspx>? portalId=4292&pageId=1411899* -- ------------------------------ Yury Polikanov, Ph.D. Associate Professor Department of Biological Sciences College of Liberal Arts and Sciences University of Illinois at Chicago 900 South Ashland Avenue, MBRB 4170 Chicago, IL 60607 Tel: 1-312-413-2408 (Office) Tel: 1-312-355-0463 (Laboratory) Fax: 1-312-413-2691 E-mail: yuryp(a)uic.edu Web-Page: *http://bios.uic.edu/bios/people/faculty/yury-polikanov <http://bios.uic.edu/bios/people/faculty/yury-polikanov>* [image: Image result for uic logo] ------------------------------

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Job opening: Scientist, Computational Chemistry
by Ying Zhang 26 Jul '21

26 Jul '21

Dear all, This post is to bring your attention to a job opportunity of a scientist position at Plexxikon Inc. We are looking for a highly motivated, computational chemist with expertise in protein structure predictions/modeling. Experience with small molecule design is a plus, but not required. Please help to distribute this to anyone that might be interested. Plexxikion (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/apply_flow/standard_applications/apply?job_id=… Please apply through the link, but not reply to this email. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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error in Download Request Form for Non-Profit Institutions
by Maxime Cuypers, Ph.D. 26 Jul '21

26 Jul '21

Hello, i get the following error: The server encountered an internal error and was unable to complete your request. Error message: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there was an error in a CGI script. tried multiple times in firefox. any idea what causes this? cheers, Dr. Maxime Cuypers Researcher, Structural Biology, St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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Problem in real space
by Firdous Tarique 26 Jul '21

26 Jul '21

Hi I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out where. Can we do something in refinement settings Or change any threshold value to avoid these problems? Input is 80S.pdb ribosome and its corresponding em map. File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff raise RuntimeError(msg) Best regards Firdous

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post-doc position at KU Leuven, ligand-gated ion channels
by Chris Ulens 26 Jul '21

26 Jul '21

A post-doctoral position is available at the Laboratory of Prof. Chris Ulens, KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of Structural Neurobiology is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our methods rely on X-ray crystallography and cryo-EM in combination with electrophysiological recordings and fluorescence-based techniques. Our laboratory hosts an integrated macromolecular crystallization facility with a Mosquito crystallization robot and two RockImagers. We have access to a 200 kV Glacios microscope on campus as well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current projects are situated at the crossroads of structural elucidation and drug discovery of different pentameric ligand-gated ion channels. We would like to recruit a post-doc with prior experience in cryo-EM or X-ray crystallography of membrane proteins. The successful candidate: - easily communicates in an open verbal manner and has a team player spirit - has an ambitious work ethic - critically contributes to writing of manuscripts and grant proposals - makes efforts to obtain independent funding - meets intermediate deadlines and brings projects to a successful end - fuels internal discussions of recent publications in the field - sets an example to younger PhD students in the lab - identifies directions for future scientific research The position is open immediately and applications will be accepted until the position is filled. Applicants are requested to submit a CV with publication list and two references. E-mail to chris.ulens(a)kuleuven.be Selection of recent publications: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4. Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511. The structural basis for an on-off switch controlling Gβγ-mediated inhibition of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117.

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Move fem map back to protein?
by Murpholino Peligro 23 Jul '21

23 Jul '21

Dear all.. How do I move a fem map back to the protein molecule? I did `phenix.fem PHASER.1-coot-1_refine_001.pdb PHASER.1-coot-0_refine_data.mtz` to generate the fem map, but when I open with coot `coot PHASER.1-coot-1_refine_001.mtz PHASER.1-coot-1_refine_001.pdb` and then file->open map->fem.cpp4... the fem map does not cover the protein (as shown in .png attached) I am not sure if this is phenix (a missing option?) or coot related ... thanks

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Ligand Library
by Christian Tüting 22 Jul '21

22 Jul '21

Dear Phenix-Team, dear Mailing-List, I have a question regarding bound ligands during refinement. In our initial structure, we have multiple spheroidenes bound (pdb ligand id SPO), but experimental data suggest that it should be speroidenones (pdb ligand id SPN). The difference between these molecules are located in an additional oxygen at the head group and a different saturation level of the carbon chain. I mananged to exchange the molecule using Coot, but during refinement I got following error: Number of atoms with unknown nonbonded energy type symbols: 602 "HETATM18420 C1 SPN B 600 .*.N C " "HETATM18421 C10 SPN B 600 .*.N C " "HETATM18422 C11 SPN B 600 .*.N C " "HETATM18423 C12 SPN B 600 .*.N C " "HETATM18424 C13 SPN B 600 .*.N C " "HETATM18425 C14 SPN B 600 .*.N C " "HETATM18426 C15 SPN B 600 .*.N C " "HETATM18427 C16 SPN B 600 .*.N C " "HETATM18428 C17 SPN B 600 .*.N C " "HETATM18429 C18 SPN B 600 .*.N C " ... (remaining 592 not shown) So, as far as I understand this error, the ligand is not in the restrained in the ligand library. I followed this tutorial: https://phenix-online.org/documentation/tutorials/elbow.html to generate the .cif file for refinement. I was just using the pdb file and the geometry from there, as it was "coot-refined" and thereby I expected the correct conformation. The refinement than run fine, but the ligand after refinement is in a complete wrong conformation and parts of the carbon chain is outside the density. I am not sure, if this is due to low resolution at these regions (which are indeed very low compared to other ligands or proteins in the map), or if during restraining something went wrong. Is it possible to add this ligand to the phenix ligand library or do you have any suggestions, how to improve the restraining using the elbow tool? Thanks in advance Christian Tüting Dr. rer. nat. Christian Tüting Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Two positions (postdoc and PhD) in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 14 Jul '21

14 Jul '21

Dear all, Just a reminder that we have two open positions (1 postdoc and 1 PhD) available to join our team and investigate metabolite transport using structural biology. Please pass along to anyone who might be interested. Thanks! PhD position = https://bit.ly/3Ak5Far Postdoc position = https://bit.ly/2SXS7Rm /Bjørn ----------------------------------------------------------------------- STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD and a postdoc position are available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective (see http://pedersenlab.dk). The projects will be developed in discussion with the selected candidates, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The projects are fully funded by the European Research Council (ERC). The candidates should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified, but start date is negotiable. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university.

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geometry_minimization makes molprobity score worse
by James Holton 13 Jul '21

13 Jul '21

Greetings all, and I hope this little observation helps improve things somehow. I did not expect this result, but there it is. My MolProbity score goes from 0.7 to 1.9 after a run of phenix.geometry_minimization I started with an AMBER-minimized model (based on 1aho), and that got me my best MolProbity score so far (0.7). But, even with hydrogens and waters removed the geometry_minimization run increases the clashscore from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one residue reaching the outlier level. Just for comparison, with refmac5 in "refi type ideal" mode I see the MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from favored to allowed, but none rise to the level of outliers. Files and logs here: https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz I suspect this might have something to do with library values for main-chain bonds and angles? They do seem to vary between programs. Phenix having the shortest CA-CA distance by up to 0.08 A. After running thorough minimization on a poly-A peptide I get: bond amber refmac phenix shelxl Stryer C-N 1.330 1.339 1.331 1.325 1.32 N-CA 1.462 1.482 1.455 1.454 1.47 CA-C 1.542 1.534 1.521 1.546 1.53 CA-CA 3.862 3.874 3.794 3.854 So, which one is "right" ? Cheers, -James

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Phenix download page not working
by Guillaume Gaullier 09 Jul '21

09 Jul '21

Hello, I am trying to download the latest phenix installer, but after I enter all the info on this page ( https://phenix-online.org/phenix_request/index.cgi ) and submit the form, I get the following error message: The server encountered an internal error and was unable to complete your request. Error message: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there was an error in a CGI script. I have not seen this reported in this mailing list yet, but my apologies to the phenix developers if they are already aware of this problem. Maybe related: I could not find anymore the simpler form in which you could check a box saying "I have registered before" so it skips the verification of your academic status and sends you a password right away. I have successfully registered before, with the same email address I am using now, and it would be convenient to still have this fast option. Thank you in advance for any help with this, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Postdoc position (Denmark), Structural biology with a focus on metabolite uptake
by Bjørn Panyella Pedersen 07 Jul '21

07 Jul '21

Dear colleagues, Please pass this open postodoc position along to anyone who might be interested. Thanks! Deadline is Aug. 15th. /Bjørn Link: https://www.au.dk/om/stillinger/job/re-advertisement-postdoctoral-position-… ---- Postdoctoral position in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark. The Pedersen group at the Department of Molecular Biology and Genetics, Aarhus University, is looking for a highly skilled and motivated postdoc with an interest in working on metabolite transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. Starting date is negotiable. The project is fully funded by the European Research Council (ERC) 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 metabolite transporting membrane proteins (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. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. 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 Department of Molecular Biology and Genetics The Department of Molecular Biology and Genetics is part of the Faculty of Natural Sciences, Aarhus University and comprises research within the areas of Gene Expression, Molecular Medicine, Structural Biology, Systems Biology and Plant Molecular Biology. There are currently 75 full time scientific staff and 120 PhD students. The department is responsible for two educations: Molecular Biology and Molecular Medicine with a yearly uptake of 160 students in total. Please refer to http://mbg.au.dk/ for further information about The Department of Molecular Biology and Genetics and to https://international.au.dk/ for information on Aarhus University, respectively. The successful candidate is offered: • Access to world-leading 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 within a surprisingly small area: 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 here for further details on the city and the university.

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Problem with modifying data type
by Stephen Cusack 05 Jul '21

05 Jul '21

Dear Phenix, Whereas in previous version of Phenix (e.g. 1 year ago) I used to be able to run Real-space-refinement for cryoEM models using either a CCP4-map or coefficients from a MTZ file , in recent versions (e.g. currently using 1.19.1-4122-000) when I load an MTZ file, it puts data type File and this stalls upon running, but the data type cannot be changed. Is this a bug or a feature (to stop you using the MTZ file) or am I doing something wrong? thanks Stephen -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org 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, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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Phenix GUI does not show (on Debian)
by Tim Gruene 05 Jul '21

05 Jul '21

Dear all, I installed phenix 1.19.2.4158 on Debian testing (version 11.0) and Debian stable (version 10.10). On Debian stable, phenix works just fine. On Debian stable (kernel 5.10.0-7-amd64), when I type 'phenix' at the command prompt, I get the usually error about the locale 'en_GB' not being available, and the Phenix splash screen, that disappears automatically. After that, nothing happens. The prompt does not return, phenix is running tg@fibonacci:~$ ps -eLF | grep phenix tg 3823 3776 3823 0 1 33859 83056 6 09:36 pts/1 00:00:00 /xtal/Suites/Phenix/phenix-1.19.2-4158/build/../conda_base/bin/python2.7 -Qnew /xtal/Suites/Phenix/phenix-1.19.2-4158/build/../modules/phenix/wxGUI2/command_line/main.py but no GUI shows up. I can use phenix through ssh on stable, so that this is not an urgent issue. I was just wondering if anyone might have a clue why phenix GUI won't show up on Debian testing? I tried two window managers, KDE and awesomewm on two different computers. Best wishes, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

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MR-Rosetta crashes during rebuild
by Andrea Piserchio 01 Jul '21

01 Jul '21

Dear all, I am trying to run MR-Rosetta using the gui; [ROSETTA_VERSION]: 2021.16+release.8ee4f02 Phenix version 1.19.2-4158 running on Ubuntu 20.04.2 LTS (20.04, focal) rosetta.run_tests seems to run without errors. As inputs, I use a HHpred file, a reflection file, a sequence (FASTA) file and I tried also providing directly the fragments files from the Robetta server. After generating some starting models, the runs keep crashing during the rebuild stage giving the error messages below. Is there a way to troubleshoot this? It does generate some initial models, so it seems to correctly read the HHPred file and the fasta file. Thank you in advance, Andrea non-zero return code: 139 Failed to run REBUILD from rebuild.log AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Segmentation fault (core dumped) from ROSETTA_CRASH.log: [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT]

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PhD position (Denmark), Structural biology with a focus on metabolite uptake
by Bjørn Panyella Pedersen 01 Jul '21

01 Jul '21

Dear colleagues, Please pass this open PhD position along to anyone who might be interested. Thanks! jobRxiv link: https://bit.ly/3Ak5Far All the best, /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective (see http://pedersenlab.dk). The PhD project will be developed in discussion with the selected candidate, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The project is fully funded by the European Research Council (ERC). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified, but start date is negotiable. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk). Deadline is July 31st 2021. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university.

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Improvement of low resolution MR phases
by Kajander, Tommi A 29 Jun '21

29 Jun '21

Hello all, I was wondering what would be current best protocols for trying to improve maps/phases for low resolution MR / refinement solutions (5-6 Å resolution). High solvent content of course, dimeric 2:2 protein complex so some NCS averaging and density modification I assume might help (related structures known, currently maps very blobby, clear solution but I think should be able to do better...). Also, refinement suggestions welcome. Best route in phenix? So far worked initially with ccp4. Other suggestions also welcome. Thanks! Tommi Tommi Kajander, Ph.D. Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki, Finland p. +358-50-4480991 http://www.helsinki.fi/kajanderlab

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Macromolecular Crystallography - CSHL Course
by Paul Adams 24 Jun '21

24 Jun '21

Dear Colleagues, The July 16th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 4 through October 19, 2021 is rapidly approaching. Please see the attached announcement, and the official course web site is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=21 please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. We anticipate holding the course in person as long as the pandemic situation continues to improve. Appropriate COVID-19 precautions will be followed to ensure the safety of all participants. Everyone will be required to provide documentary proof of a prior FDA or EMA approved vaccine. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2021 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO), Tom Peat (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be data collection at state-of-the-art beamlines at NSLS-II. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This course is supported with funds provided by the National Institute of General Medical Sciences for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tom, Tassos, Paul, and Jim > Begin forwarded message: > > From: Cold Spring Harbor Laboratory Meetings & Courses <meetmail(a)cshl.edu> > Subject: Macromolecular Crystallography - CSHL Course > Date: June 24, 2021 at 5:20:20 AM PDT > To: pdadams(a)lbl.gov > Reply-To: meetmail(a)cshl.edu > > > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > October 4 - 19, 2021 > Application & Materials Deadline: July 16 > We anticipate that the vaccine situation may sufficiently improve to allow us to offer this course safely in-person. > > All participants will be required to provide documentary proof of a prior FDA or EMA approved vaccine. > Instructors > Janet Newman, CSIRO, Australia (likely remote) > James Pflugrath, Rigaku Americas Corporation (ret.), Texas > Anastassis Perrakis, Netherlands Cancer Institute > Paul Adams, Lawrence Berkeley National Laboratory > Co-Instructor: > Tom Peat, CSIRO, Australia(likely remote) > X-ray crystallography has been the cornerstone of structural biology for half a century, and remains the technique of choice for atomic resolution understanding of macromolecules and for structure guided drug discovery. This intense course combines laboratory and computational instruction to train course participants in the major techniques used to determine three-dimensional structures. It is designed for scientists with a working knowledge of protein structure and function, but who are new to macromolecular crystallography or who wish to increase their in-depth knowledge of macromolecular crystallography. > Topics to be covered include > Basic diffraction theory > Crystallization (proteins, nucleic acids, complexes and membrane proteins) > Synchrotron X-ray sources and optics > Data collection and processing > Structure solution by experimental phasing methods (SAD, MAD, MIR, and others) and molecular replacement > Electron density maps improvement > Model building and refinement > Structure validation > Coordinate deposition > Structure presentation > If you are interested in applying for this course please let us know by submitting the Expression of Interest form via the course website as soon as possible. > Please click this link to go to the Macromolecular Crystallography course website for further info. <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > > > Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 > -- 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) Member of the Graduate Group in 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 <http://cci.lbl.gov/paul> ORCID: 0000-0001-9333-8219 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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Re: [phenixbb] [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
by David Briggs 22 Jun '21

22 Jun '21

Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link). If the second H is added, this breaks the refinement of the Asn-NAG bond. My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box. I hope this fixes your problem. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs ________________________________ From: CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> on behalf of Jiang Xu <foxjuly(a)GMAIL.COM> Sent: Tuesday, June 22, 2021 6:47:36 AM To: CCP4BB(a)JISCMAIL.AC.UK <CCP4BB(a)JISCMAIL.AC.UK> Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine External Sender: Use caution. Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? [image.png] Thank you, Best, Jiang Xu Lin Chen's Research Group University of Southern California ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscm…> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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Macromolecular Crystallography School 2021
by Nicole Larrieux 21 Jun '21

21 Jun '21

Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School 2021 "Structural Biology to enhance high impact research in health and disease” to be held from Sep 20 to Oct 1, 2021 Please find the application form and further information at http://pasteur.uy/novedades/mx2021/ The application deadline is June 30, 2021. For further inquiries contact mx2021(a)pasteur.edu.uy Main Topics: · data collection (remotely @ Diamond synchrotron); · data processing; · phasing and structure determination; · model refinement and validation. 25 participants will be selected, prioritizing advanced PhD students, postdocs and young researchers. No registration fee, please look in the www site for details on application procedures. Participants will have the opportunity to collect data from their own crystals at Diamond Light Source synchrotron via remote access, with the assistance of Diamond staff. The workshop will be virtual considering the pandemics constraints. It will combine excellent lectures with hands-on problem-solving sessions. Tutorials of state-of-the-art software will include XDS, Dials, Phaser, ShelX, Coot, Refmac, Buster-TNT, PISA, among others. Since the workshop is virtual additional participants may elect to attend lectures only. If you wish to do this please complete the registration form and indicate that this is your choice. Invited speakers and tutors: • Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil) • Kevin Cowtan (University of York, UK) • Eleanor Dodson (University of York, UK) • Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK) • Elspeth Garman (University of Oxford, UK) • Richard Garratt (Instituto de Física de São Carlos, Brazil) • Beatriz Guimarāes (Instituto Carlos Chagas Fiocruz, Curitiba, Brazil) • Marin van Heel (Lab. Nacional de Nanotecnologia CNPEM, Campinas, Brazil) • Ronan Keegan (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Eugene Krissinel (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Andrey Lebedev (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Natalia Lisa (Instituto de Biología Molecular y Celular, Rosario, Argentina) • Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK) • James Parkhurst (Diamond Light Source, Didcot, UK) • Randy Read (University of Cambridge, UK) • Silvia Russi (Stanford Synchrotron Radiation Lightsource, USA) • Nukri Sanishvili (Argonne National Laboratory, Chicago, USA) • Isabel Usón (Instituto de Biología Molecular de Barcelona, Spain) • Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK) Organizers: Nicole Larrieux, Clinical Biochemist. Institut Pasteur de Montevideo, Uruguay Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); and the Programa Iberoamericano de Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES consortium. Looking forward to seeing you at the Workshop! Nicole, Alejandro, Kyle and Ronan Nicole Larrieux Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/research/labs/molecular-and-structural-microbiology-lab

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Phenix.real_space_refine crash
by Reza Khayat 18 Jun '21

18 Jun '21

Hi, Two files are attached regarding my constant crashing during global minimization. Any help would be appreciated. Refinement is run using the run_Rama_Clash_ss_v1.18.2-3874.eff file. ? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Real space refinement not recognizing modified bases from ribosome
by Firdous Tarique 16 Jun '21

16 Jun '21

Hi I am trying to do real space refinement of a 40S rigid body docked model in a cryoEM map of 4.8 Angstrom resolution. The PDB contains some modified nucleic acid bases due to which the program ends with the following error. Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols; 52 Please edit the model file to resolve the problems and /or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Seems its refinement library is not able to read the modified bases. Can you please advise how to fix this problem. What is the best way to update the library ? Any suggestions are highly appreciated. Best Firdous

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Postdoc position in structural biology at UT Health San Antonio
by Yogesh Gupta 16 Jun '21

16 Jun '21

*Postdoctoral Fellow position at UT Health School of Medicine, San Antonio, Texas* The laboratory of Dr. Yogesh Gupta (http://ccri.uthscsa.edu/YGupta.html) at the University of Texas Health at San Antonio is seeking an enthusiastic Postdoctoral Fellow to study structures and function of RNA modification and chromatin remodeling complexes. We use structural biology (X-ray, NMR, cryo-EM) and cell-based methods to address basic mechanistic questions in viral pathogenesis and pediatric cancers. Gupta laboratory provides a rich multi-disciplinary training environment and access to cutting-edge technologies in structural biology and drug development. Further details of our most recent work can be found here: 1. Nature Communications. 2021 Jun 2; 12: 3287. PMID: 34078893. doi: 10.1038/s41467-021-23594-y <https://www.nature.com/articles/s41467-021-23594-y> 2. Nature Communications. 2020 Jul 24;11(1):3718. PMID: 32709886. doi: 10.1038/s41467-020-17496-8 <https://www.nature.com/articles/s41467-020-17496-8> Preference will be given to applicants with demonstrated experience in protein purification from insect/mammalian cells and structural characterization of protein-nucleic acid complexes by X-ray crystallography or cryo-EM. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work independently but also effectively and collaboratively as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in a related discipline and have no more than 2 years of postdoc experience. The Greehey Children’s Cancer Research Institute (GCCRI) is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. The GCCRI has significant external funding, a large endowment from the state, and links to philanthropic entities. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill County. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry. There is no state income tax in Texas. All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities. Salary is competitive and commensurate with experience. If interested in applying, please send a short description of your research accomplishments and a CV with contact information of 3 references to Dr. Yogesh Gupta (email: guptay(a)uthscsa.edu). Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center San Antonio 8403 Floyd Curl Drive, San Antonio, TX, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Error in Dock in Map
by Firdous Tarique 15 Jun '21

15 Jun '21

Hi I am trying to fit a 40S ribosomal subunit obtained from PDB into a 5 Angstrom EM map using the Dock in Map module. However the program ends with the following error. Model contains both protein and rna/dna atoms.....only one chain type allowed. How can I fix this problem? Any suggestions? Regards Firdous

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C-C sugar linkage in real-space refinement
by Kevin Jude 14 Jun '21

14 Jun '21

I'm trying to refine a cryoEM structure that contains some MAN/C1-TRP/CD1 glycosylations. I've done this successfully in crystallographic reciprocal space refinement, using cif files to define the MAN geometry and the MAN-TRP linkage, plus adding LINK instructions to the pdb file. In this cryoEM structure, though, using the same .cif definition files and similar LINK instruction, the bond is still not defined in the .geo file and instead it's treated as a nonbonded interaction, kicking the mannose away from the indole side chain. The NAG-ASN linkages in the cryoEM structure are fine. Do I need to do anything differently to define these linkages in Real Space Refine compared to phenix.refine? -- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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