- phenixbb - phenix-online.org

Using AutoBuild to Complete a Model
by Whitley, Matthew J 18 Aug '21

18 Aug '21

Hello all, I have a very large protein with 16 copies in the asymmetric unit (nearly 15,000 total residues). Upon initial model building, ~30 residues at the N-terminus of each identical chain were not built. After building the reliable parts of the model and filling in other gaps and then refining that partial (but nearly complete) model, the N-terminal density has now improved to the degree that I can manually build a number of the missing residues in Coot. However, that means manually building the same series of residues over and over for each of the 16 identical chains. Is there a way to get AutoBuild to add these N-terminal residues for me to spare me the tedium of repetitive manual building? What I’ve gleaned from the documentation so far: >From the phenix.fit_loops documentation, it seems like that tool only works for filling in chain breaks, i.e. there is already modeled protein at each end of the missing region. That’s not the case for me because I’m trying to work backward toward the N-terminus. If I am reading the phenix.autobuild documention correctly, it sounds like there are two modes: (i) Standard mode - rebuild the whole protein from scratch, which does give the possibility of adding my N-terminal residues. However, I don’t want my nearly complete existing model to be rebuilt, I just want AutoBuild to try to add the missing N-terminal sequence to the existing model. (ii) Rebuild-in-place, which rebuilds the current model but doesn’t add or subtract any atoms. So that sounds like it’s not what I’m looking for because it won’t add the N-terminal sequence AND it rebuilds the existing model, which I want to keep exactly as is. Is there some series of options in AutoBuild that will allow me to just add missing residues (provided in the sequence file) but keep all the other currently existing residue in the input model exactly as they are? Happy to hear any advice you can give. Thanks, Matthew --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

3 3

Post-doctoral fellow (M/F) in molecular and structural biology (Cryo-EM)
by Philippe Bénas 13 Aug '21

13 Aug '21

*/Posted on behalf of Dr. Franck Martin (CNRS IBMC, Strasbourg, France)/* */Please reply to F.Martin(a)ibmc-cnrs.unistra.fr/* */ /* */======================================================================================= /* */ /* */URGENT - Recovery Plan Project - Post-doctoral fellow (M/F) in molecular and structural biology (Cryo-EM)/* *Mission*** /You will be working as a post-doctoral researcher in a mixed public/private environment. The team 'Evolution of translation initiation systems in eukaryotes' of the unit 'Architecture and Reactivity of RNA' (UPR 9002 of the CNRS) of the Institute of Molecular and Cellular Biology (IBMC) of Strasbourg in association with the company Novalix. NovAliX is a 180+ employees society based in Illkirch (near Strasbourg). We offer to the pharmaceutical industry a complete range of services spanning biophysics, biochemistry, structural biology, chemistry & drug discovery. It is specified that this recruitment offer is part of the France Recovery Plan on a research collaboration project with a company which will be submitted to the DRARI for validation. The project will consist in structurally and functionally characterizing macromolecular complexes allowing the initiation of viral RNA of SARS-CoV-2. / *Activities* /The approaches used will be based on the use of cell-free translation extracts that will allow us to assemble and purify translation initiation complexes on our model messenger RNAs. The composition of these complexes will be determined by mass spectrometry and their structure by advanced structural approaches.The techniques used will be: / // /- Biochemical and molecular biology methods dedicated to the study of proteins and nucleic acids and in particular RNA/ /- Cryo-EM sample preparation, optimizing sample vitrification conditions./ /- Collect and analyse cryo-EM data. 3D reconstruction, structure determination and atomic model building./ /- Preparation of in vitro cell-free translation extracts/ // /The candidate will have to develop his/her project independently./ *Expected qualifications and proficiencies* /This includes the mastery of biochemical and molecular biology approaches for the purification of ribonucleoprotein complexes. Strong expertise in structural biology (Crystallography/Cryo-Electron Microscopy) especially on macromolecular complexes containing the ribosome will be considered as a plus. Ideally, the candidate should also be able to interpret electron density maps to establish atomic models of ribonucleic complexes containing the ribosome. The candidate must have defended his/her thesis in 2019 or 2020. / *Environment* /The candidate will join a biochemistry and molecular biology team specialising in translation initiation in eukaryotes. The structural part of the project will be implemented within the company Novalix. The Novalix cryo-EM platform is currently equipped with a Glacios microscope outfitted with a phase plate, Falcon 3 camera and microED setup. The candidate will spend 20% of his/her time in the public laboratory for the preparation of samples and 80% of his/her time at Novalix for the structural aspect./ More on IBMC: https://ibmc.cnrs.fr/en/ More on Strasbourg: https://www.visitstrasbourg.fr/en/welcome-in-strasbourg/ More on Alsace area: https://www.visit.alsace/en/ *Work constrains and professional risks* /The project will require the manipulation of radioactivity and the synthesis of RNA.Therefore, the mastery of good laboratory practices will be considered a plus./ *Application* /Applications will only be made via the recruitment website but feel free ton contact Dr. Franck Martin for any further details including application rules./ /Application website:/ /https://emploi.cnrs.fr/Offres/CDD/UPR9002-FRAMAR-006/Default.aspx?lang=EN/ *Salary* /Gross salary will be between 2675 and 3767 € per month according to working experience./ *Contact information*: /F.Martin(a)ibmc-cnrs.unistra.fr/

1 0

experienced protein crystallographer needed
by Mooers, Blaine H.M. (HSC) 12 Aug '21

12 Aug '21

Dear all, Please share this job announcement with potential candidates. Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Assistant Professor of Research level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography. The candidate will not be expected to write grant applications. Pluses in a candidate's background include experience with membrane protein purification and LCP crystallization, experience with Cyro-EM, or experience with other structural biology methods. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The BSC has contributed to the awarding of 23 million dollars in grant funding and 33 publications in the past nine years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC will be a vital part of a new Center for Therapeutic Science. The center will coordinate and foster the drug development pipeline with the BSC playing a central role in structure-based drug design. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer. Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at ouhsc.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

1 0

Molprobity and D-amino acids
by Prasun Kumar 10 Aug '21

10 Aug '21

Hi All I am trying to solve a structure with D-amino acids. After refinement when I check the Molprobity results, I find a lot of C-beta outliers (a snapshot is appended below). I also get clashes between the carbonyl group of one residue and the side chain of the other. Any suggestion would be really helpful. C-beta outlier [cid:df63696e-1ce2-496d-9c9d-f4d35bd16015] Clashes [cid:9f665070-525b-497c-8009-e55ba533fdc1] Cheers PK

2 1

Overall map resolution (d_FSC) x local map resolution
by Carlos HENRIQUE FERNANDES 09 Aug '21

09 Aug '21

Dear all, I've been finding some discordance between overall map resolution value obtained at phenix.mtriage (d_FSC) and local map resolution values obtained at phenix.local_resolution. phenix.mtriage (using full map and both half maps) provides a d_FSC of 4.31 Å; however, the phenix.local_resolution (using both half maps and not informing the d_FSC) provides local map resolution values have a range of 3.8 - 4.4 Å with most of the map having 4.0 Å resolution with very few parts (only small flexible regions at terminal regions) having 4.3-4.4 Å resolution. Are these differences normal or is there something wrong with my map refinement? Despite d_FSC being 4.31 Å; can I consider my map at 4.0 Å resolution and do the sharpening and dock in map operations at 4.0 Å? Thanks in advance, Carlos Fernandes

3 2

Postdoc position available
by Tobias Beck 05 Aug '21

05 Aug '21

Dear all, We have an opening for a Postdoc position in my group. The Beck group is located at the University of Hamburg, with labs well-equipped for nano chemistry and protein chemistry, and supported with computational infrastructure for protein design. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. The project will focus on machine learning approaches to guide the redesign of protein containers. Towards this goal, previous knowledge on protein assemblies and crystal structures will be be implemented. Identification of suitable models will be carried out to connect the assemblies to surface properties of proteins. The position is available starting on October 1st 2021. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=8d3f1e2… Link to the group homepage: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html Deadline for applications is August 16 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/ ____________________________________________________________

1 0

(no subject)
by Smita Yadav 30 Jul '21

30 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

4 5

Visiting Research Specialist Position | Polikanov Lab | University of Illinois at Chicago
by Yury Polikanov 28 Jul '21

28 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] ------------------------------

1 0

Job opening: Scientist, Computational Chemistry
by Ying Zhang 27 Jul '21

27 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

1 0

error in Download Request Form for Non-Profit Institutions
by Maxime Cuypers, Ph.D. 27 Jul '21

27 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

2 1