- phenixbb - phenix-online.org

Phenix opens COOT but does not load map or model
by Boniecki, Michal 08 Sep '21

08 Sep '21

Hello, I used to be able (with previous phenix versions) load models into COOT after refinement. Now when I click open in COOT, only COOT window is open but neither maps or model are loaded.Also there is no "connected to phenix' displayed in COOT sidebar I have no problems with loading and displaying both in phenix or pymol (open with phenix or open with pymol buttons). Any suggestions how to solve it would be appreciated. COOT 0.9.5, phenix 1.19.2-4158 Michal

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Job posting: Scientist (crystallography) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 08 Sep '21

08 Sep '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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IUCr’s Committee on Data recent meeting minutes now online
by John R Helliwell 06 Sep '21

06 Sep '21

Dear Colleagues, I imagine that you will be interested in the IUCr’s Committee on Data recent meeting minutes which are now online here:- https://forums.iucr.org/viewtopic.php?f=39&t=441 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman IUCr Committee on Data

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copy R-free array from reference mtz using command line?
by Aaron Thompson 30 Aug '21

30 Aug '21

PhenixBB, I know this can be done via GUI, but is it possible to copy the R-free array from a reference mtz to a new mtz using the command line? I don’t see this as an option in phenix.reflection_file_converter. Thank you, Aaron

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NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

Hi, I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Re: [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

9 am CEST (Norway). Pretty early for our North American colleagues, especially those on the west coast! > On 27 Aug 2021, at 05:18, Robert Rose <rbrose2(a)ncsu.edu> wrote: > > Does the workshop start on August 31 at 9 am GMT? > > On Thu, Aug 26, 2021 at 2:27 PM Randy John Read <rjr27(a)cam.ac.uk> wrote: > Hi, > > I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: > > https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html > > I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 336827 > Hills Road E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Peptide bond to symmetry related molecule
by Damian Ekiert 23 Aug '21

23 Aug '21

Hi All, We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers. Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond. Thanks for your help! Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert(a)ekiertlab.org www.bhabhaekiertlab.org

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Postdoctoral position in Computational Biochemistry
by Yasser Almeida 23 Aug '21

23 Aug '21

Dear all, The group of Computational Biochemistry of Prof. Elsa Sánchez-García at the University of Duisburg-Essen is announcing a Postdoc position focused on the computational design of chemical tools and inhibitors for the study of proteins and protein-protein interactions involved in cell state transition. The deadline for applications has been changed to September 30th. More information can be found at https://www.uni-due.de/computational-biochemistry. Best regards, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez(a)uni-due.de <%20yasser.almeida-hernandez(a)uni-due.de> Phone: +49 201 183 2457

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Project Scientist and Postdoctoral research positions in XFEL, ML, and material science computational methods
by Aaron Brewster 18 Aug '21

18 Aug '21

Hello, I'm excited to announce that two positions are immediately open in my group in the fields of material science, serial X-ray crystallography, and machine learning. Links to postings: Computational Project Scientist - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93507 Computational Postdoctoral Scholar - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93506 In these exciting roles, you will work in the Molecular Biophysics and Integrated Bioimaging Division on a project that will research adding advanced spatial and symmetry aware neural network training methods to small-molecule chemical crystallography and material science data processing. This will use AI methods developed as part of a close collaboration between teams at Lawrence Berkeley National Labs (LBNL), University of Connecticut, and MIT. The larger group is researching crystal engineering of hybrid coordination polymers towards achieving rational control over the optoelectronic properties of low-dimensional nanostructures. These positions are focused on the chemical crystallography aspect of the program, but the successful candidates will be expected to participate in all aspects of the program, including data collection at X-ray free electron lasers worldwide, data analysis on supercomputing facilities, structure solution, research on AI driven structure prediction, paper writing, and software management. Both roles are 3 year appointments. This work will be part of the Department of Energy Integrated Computational and Data Infrastructure for Science <https://insidehpc.com/2021/08/doe-funds-15m-for-integrated-computational-an…> Research program. Specific details follow. Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) <https://diversity.lbl.gov/ideaberkeleylab/> and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab’s mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. *Computational Project Scientist* *What You Will Do:* - Design and train neural networks that allow determination of the unit cell and crystal orientations of small molecule crystals from sparse, randomly oriented diffraction patterns. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Research methods to scale training and use of these neural networks on multiple nodes in high performance computing environments. - Lead data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. - Assist Principal Investigator in developing grant proposals. - Document and maintain existing and new data processing software, including the cctbx build system. *What is Required:* - 2-5 years of relevant experience beyond the highest degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - A strong background in Python, C++, or an equivalent platform for scientific computing. - A track record of critical thinking, problem solving, and mathematical intuition, demonstrated through publications and presentations. *Desired Qualifications:* - Familiarity with general Python scientific data packages such as NumPy, SciPy, and pandas. - Versed in modern coding practices for scientific computing, including algorithm design and evaluation, source code management under a revision control system like git, and incorporation of readable documentation and comments. - Expertise in computational approaches in at least one of the areas related to the research is required, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Familiarity with small-molecule material design and synthesis. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. *Computational **Postdoctoral Scholar* *What You Will Do:* - Design and train neural networks to model diffraction from small molecule crystals. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Assist in data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. * What is Required:* - PhD degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - Experience in computational approaches in at least one of the areas related to the research, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. * Desired Qualifications:* - Familiarity with Python, C++, and general scientific data packages such as NumPy, SciPy, and pandas. - Familiarity with small-molecule material design and synthesis. Please do not hesitate to reach out to me for more information. Thank you, Aaron S. Brewster, PhD Computational Research Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Specifying import-time dependencies in _ext libraries?
by Russell M. Taylor II 18 Aug '21

18 Aug '21

I've developed an mmtbx_probe_ext module that makes use of objects defined in iotbx_pdb. I've added that library to LIBS= in the SConscript file, and it is able to link and run properly. However, when a Python script imports mmtbx_probe_ext, that load fails unless the same script has previously imported from iotbx: The following works: from iotbx.map_model_manager import map_model_manager import mmtbx_probe_ext as probe But the following fails: import mmtbx_probe_ext as probe from iotbx.map_model_manager import map_model_manager ImportError: /home/taylorr/rlab/cctbx-reduce-python27/build/lib/mmtbx_probe_ext.so: undefined symbol: _ZNK5iotbx3pdb9hierarchy5chain5atomsEi How do I tell Sconscript (or what do I do in my _bpl file) to tell Python that it needs to load the other module first? Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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Postdoc position in San Antonio, TX
by Yogesh Gupta 17 Aug '21

17 Aug '21

Dear Colleagues: My laboratory at the University of Texas Health Science Center at San Antonio is seeking an enthusiastic Postdoctoral Fellow to work on an NIH-funded project on SARS-CoV-2 and RNA modification. We will use X-ray crystallography, cryo-EM, and cell-based methods to address basic mechanistic questions and develop novel antivirals. These two papers describe our most recent work on SARS-CoV-2. 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> 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 purification and structural characterization of protein-nucleic acid complexes by X-ray crystallography with a strong interest in learning cryo-EM. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 3 years of postdoc experience. Salary is competitive and commensurate with experience. 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. 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 Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, TX, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Using AutoBuild to Complete a Model
by Whitley, Matthew J 17 Aug '21

17 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

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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/

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experienced protein crystallographer needed
by Mooers, Blaine H.M. (HSC) 11 Aug '21

11 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

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Molprobity and D-amino acids
by Prasun Kumar 09 Aug '21

09 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

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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

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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/ ____________________________________________________________

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(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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