- phenixbb - phenix-online.org

Phenix.Refine fix WXC has no effect
by White, Mark 17 Aug '20

17 Aug '20

Hello, I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc. Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement. Am I missing something? Best regards, Mark Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, Manager, SCSB Macromolecular X-ray Laboratory UTMB, Galveston, TX http://xray.utmb.edu

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Phenix.refine on coordinate-optimised structures
by Joey Farrell 07 Aug '20

07 Aug '20

Hello, I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol. I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors of such structures while preserving their earlier optimisation in real space. I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software that I am not yet aware of. Thank you for your help! Best, Joey

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Phenix Real_Space_Refine and Torsion NCS restraints
by Mark A. White 04 Aug '20

04 Aug '20

Hello, Are there plans to include Torsion Angle NCS restraints in the Phenix.Real_Space_Refine module? At low resolution (~ 3-4Å) I would like to include NCS restraints, but my molecule is flexible and the strict NCS constraints used in the Real_Space_Refine module are not appropriate. I am currently using phenix-1.18.2-3874. Best regards, Mark

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map to model - DNA model building
by Manoj saxena 04 Aug '20

04 Aug '20

Hello, I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the map to model in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the map as a .ccp4 file. However the output model fitted in the map I am getting is many fragmented PDB files and only one chain of DNA. What is the best way to get a higher fraction of the DNA model fitted into the map, can I switch off the segmentation of map and get both strands fitted into the map. Or the only option is to manually build? Thanks for your help Regards Manoj Saxena

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Model moving out of map
by Shanti Pal Gangwar 03 Aug '20

03 Aug '20

Dear all, I am trying to refine a Cryo-EM map at a decent resolution. The model was fit into the map in chimera and refined against the same map in Real space refinement in Phenix but after the run, a significant part of the model moved out of the density. I would appreciate any suggestion/strategy to solve this issue. Thank you Shanti Pal

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Postdoc position at UT Health Science Center, San Antonio, Texas
by Yogesh Gupta 02 Aug '20

02 Aug '20

The laboratory of Dr. Yogesh Gupta at University of Texas Health Science Center in San Antonio is seeking an enthusiastic Postdoctoral Fellow to study the structure and function of nucleoproteins in infectious diseases and cancer. We combine structural biology tools (X-ray, cryo-EM, NMR) with cell-based methods to address mechanistic questions and exploit this knowledge for drug development. Please visit below websites to learn about our research program – https://www.nature.com/articles/s41467-020-17496-8 *http://ccri.uthscsa.edu/YGupta.html <http://ccri.uthscsa.edu/YGupta.html>* Preference will be given to applicants with demonstrated experience in macromolecular crystallography. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work as part of a team. 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 2 years of postdoc experience. Salary is competitive. San Antonio offers affordable cost of living and there is no state income tax in Texas. If interested in applying, please send a short description of your research accomplishments, and CV with a list of 3 references to Dr. Yogesh Gupta (email: *guptay(a)uthscsa.edu <guptay(a)uthscsa.edu>*). The Greehey Children’s Cancer Research Institute 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. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry.* 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.* Thank you very much for your time. Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, Texas, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Fwd: Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Greater Boston, MA)
by yanfeng zhou 31 Jul '20

31 Jul '20

If you have strong interest in one of the following areas, please continue to read and check the link for more details. 1. Developing new algorithms to revolutionize biologics discovery 2. Challenging yourself with large and unique datasets and converting your learnings to tools/products that can help patients 3. Engineering of antibody, nanobody, and other biotherapeutics modalities 4. Learning how scientists from various training backgrounds collaborate together to discover and deliver faster and better biologics treatments. The Protein Engineering group within Sanofi Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position. We use leading-edge structural biology and computational tools to support biologics project needs from Sanofi’s multi-targeting, multi-modality research pipeline. Our team has a great track record of patents and publications, including Science, Nature Cancer, and Nature Communications, in the area of biologics characterization, antibody engineering and multi-specific antibodies. This postdoc project will focus on developing a machine learning approach to predict epitope-paratope, given any antibody-antigen pair, by combining in-depth understanding of structure biology, antibody engineering, and large datasets both internally and externally. The successful candidate will be with Ph. D. degree in related area and has an advanced understanding and practical experience with developing and applying complex machine learning solutions for structural biology data. The successful candidate will gain deeper insight into drug development process and transform AI/ML algorithms into accelerating biologics discovery and development process. Application Link: https://sanofi.wd3.myworkdayjobs.com/en-US/StudentPrograms/job/Framingham-M… *About Sanofi:* Every day, Sanofi's 100,000 employees are committed to improve the lives of people around the world, with sustainable and responsible solutions and initiatives. Sanofi is recognized as one of the leading biopharmaceutical companies in the world and is pioneering innovation in biologics with the first approved nanobody drug, the first clinical stage tri-specific antibody, and a novel genetic codon expansion platform for new engineering capabilities. Details of the organization and the company’s mission and goals can be found on our website (http://www.sanofi.us/l/us/en/index.jsp). ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Yanfeng Zhou, Ph.D. Email: YanfengZhou.pku(a)gmail.com <yanfengzhou.pku(a)gmail.com>

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postdoctoral position at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 29 Jul '20

29 Jul '20

The Bahl Lab <http://function-structure.org/> at the Institute for Protein Innovation (IPI) in Boston is recruiting Postdoctoral Fellows. We use protein design to accelerate drug discovery and to engineer new lead therapeutic molecules. In addition to traditional academic collaborations, we work closely with pharmaceutical and biotech companies, as well as venture capital firms. We are looking for translationally-minded scientists who want their work to have a direct impact on the world. We will provide training in computational protein design using Rosetta, including de novo protein design and the design of protein function and biophysical properties. Postdoctoral Fellows at IPI leverage our high-throughput automated laboratory infrastructure. We are especially excited to expand our work in the following research areas: - prediction and design of protein developability for therapeutic applications - engineering of de novo miniprotein/peptide lead therapeutics for oncology, infectious disease, hypertension and diabetes, etc. - antibody design, including de novo paratope design - enzyme design Strong candidates will have demonstrated expertise in one or more of the following: - protein biochemistry: protein production and biophysical characterization, enzymology - structural biology: cryo-EM, X-ray crystallography, NMR - immuno-oncology: cell culture models, fluorescence activated cell sorting - traditional protein engineering: directed evolution, library construction, yeast and/or phage display - computational biology: machine learning, data science, molecular dynamics and/or modeling If you are excited to join a team of protein designers working to tackle audacious projects aimed directly at improving human health, please send your CV to: chris.bahl(a)proteininnovation.org About IPI The Institute for Protein Innovation is a non-profit organization that is advancing protein science to accelerate research and improve human health. The Institute is located at Harvard Medical School. IPI uniquely combines the freedom of academic exploration with the high-throughput scaling of industry to take on transformative protein-based initiatives that no other laboratory or organization can or will pursue. IPI is deploying state-of-the-art technologies to build a repository of powerful protein tools and reagents and share them through licensing and collaboration. These will enable new biomedical and therapeutic discovery for researchers in academia and industry alike. This constellation of vanguard technology and expertise positions IPI to train the next generation of entrepreneurs and protein scientists to lead the discovery of new medicines. The IPI is an equal opportunity employer and prohibits discrimination based on ethnicity, religion, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, socioeconomic status, marital or veteran status, etc. Candidates from underrepresented backgrounds are especially encouraged to apply. -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

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Re: [phenixbb] Phaser-MR output after each component placement
by Randy Read 28 Jul '20

28 Jul '20

Hi Boaz, At the moment, that is indeed the only thing you can do with the partial solution information from the log file. In the CCP4 environment, you can cut and paste lines from the log file to make a .sol file, and use that to run something like a refinement job to produce a PDB and MTZ for a partial solution, but the Phenix environment uses Python pickle files to store the transformations, so that option doesn’t apply. (Unless you run Phaser from a script, in which case the Phenix and CCP4 versions work the same.) At one point, Phaser was writing out a PDB file for the top solution at every point in the process, but we felt that led to clutter and that it was confusing. There’s a major rewrite going on at the moment, and the new phasertng will primarily be run through the phaser.voyager pipeline. One of the design criteria here was to be able to examine branches that weren’t taken or intermediate points in the ongoing search, and to be able to work with them while the overall job is still running. So there will be a better option in the hopefully not too distant future! Best wishes, Randy ----- 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 > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > The closest option that comes to mind to do what you're looking for is to take the Euler angles+translations for each of the monomers in the .sol file (or at the top of the final pdb file) and apply each of them to the initial model using any transformation program of your choice. > I am more familiar with running Phaser using the ccp4 gui but it shouldn't be very different under Phenix. > Phaser people may well suggest a more elegant option. > Stay safe, > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer(a)gmail.com> wrote: > Dear phenix board, > > does anyone of you know if there is an option in phaser-MR to output a pdb after each placed component? > For example: I suspect there to be 5 molecules in the AU. I start a replacement with 5 molecules and phaser places 1 (I would like to inspect that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so on... > Is that possible? I couldn't find the option in the gui or in the phenix documentation, but maybe in the CLI? > I know I can run one after the other, but that would potentially waste CPU time until I find time to inspect them. > > Cheers, > Johannes > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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Visiting Research Specialist Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 27 Jul '20

27 Jul '20

The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the *Visiting Research Specialist* position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov's research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). The successful candidate will be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Basic qualifications:* - BS degree in chemistry, biochemistry, biophysics, or a related field; - MS 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 is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://jobs.uic.edu/job-board/job-details?jobID=133847 by August 14, 2020. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act.

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Phaser-MR output after each component placement
by Johannes Cramer 27 Jul '20

27 Jul '20

Dear phenix board, does anyone of you know if there is an option in phaser-MR to output a pdb after each placed component? For example: I suspect there to be 5 molecules in the AU. I start a replacement with 5 molecules and phaser places 1 (I would like to inspect that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so on... Is that possible? I couldn't find the option in the gui or in the phenix documentation, but maybe in the CLI? I know I can run one after the other, but that would potentially waste CPU time until I find time to inspect them. Cheers, Johannes

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Adjusting pixel size using phenix
by Noor Agip 23 Jul '20

23 Jul '20

Hi, Is there a way to adjust pixel size of a volume in phenix? I have been using ResolveCryoEM and I would now like to calibrate the pixel of the resulting map. This could be done in chimera but requires resampling the map to a RELION map of the correct pixel size. Best wishes, Noor

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Heme geometry restraint
by Yangqi Gu 21 Jul '20

21 Jul '20

Dear all, I have a question regarding the heme c geometry restraint. I am aware that heme c could undergo distortion when bound to protein, but I am not sure at what resolution I could claim such distortion (such as ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I did the refinement in phenix with real space refinement, some of the hemes are distorted and I am wondering if it is justified to leave it that way or do I have to impose the flat plane geometry. If so, how should I proceed to impose such geometry? Thank you in advance! Best, Yangqi

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mr_rosetta question
by Wei Wang 18 Jul '20

18 Jul '20

Dear all, I would like to get help on a mr_rosetta run. I have a case that 5 copies of searching model was found by Phaser, and I would like to find the sixth one. In addition I would like to improve the building of the MR solution. In such case I’m considering a mr_rosetta run, with some parameters like this: phenix.mr_rosetta seq_file=seq.dat search_models=placed_5_copies.pdb already_placed=true ncs_copies=1 … My question is, should I use the already placed 5 copies model as search_models, with ncs_copies=1, or should I use the original searching model with ncs_copies=6 (in this case I guess I should get rid of the other four copies from the result of Phaser)? For seq.dat, should I use the sequence from one copy of searching model, or paste 5 copies into the seq.dat? Thanks, Wei

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ligand possibly bound to active site cysteine
by Jorge Iulek 18 Jul '20

18 Jul '20

Dear all, I am refining a structure of a Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (converts glyceraldehyde 3-phosphate into D-glycerate 1,3-bisphosphate) , https://www.brenda-enzymes.org/enzyme.php?ecno=1.2.1.12 . <https://en.wikipedia.org/wiki/Glycerate_1,3-bisphosphate> It turns out that its active center cysteine presents bound ligands , covalently or not to be determined if possible (data resolution 2.51 A). I would like to get help on two issues, (1) what the ligand might be and (2) how to treat it (correct me) in phenix.refine. 1) The protein was expressed in E. coli; it had much contact with glycerol and crystallization conditions include the "ethylene-glycols-mix" ("a mixture of diethylene glycol, triethylene glycol, tetraethylene glycol, and pentaethylene glycol"). Nevertheless, no NAD cofactor was added, and there is no electron density for it. Otherwise, phosphate was also present in crystallization condition. In a previous study, I learned that glycerol might also contain minor amounts of ethylene glycol. I wonder, nevertheless, about glyceraldehyde (and note resemblance with the substrate). Catalytic mechanism includes a hemithioacetal intermediate (https://febs.onlinelibrary.wiley.com/doi/abs/10.1046/j.1432-1327.1998.25204… ) such that cysteine SD is bound covalently to a carbon. I wonder also how much this might attack an ethylene glycol and their likes. Pictures for the density are shown at for the 4 monomers of the a. u., first 4 photos: https://photos.app.goo.gl/Y7MyugqwRFD4sjgDA (blue 1 sig for e. d. maps, green 3 sig for Fourier difference maps) . Density is different among them to different degrees. The nearby threonine, in some cases, seems to interact with a blob (and it is helped by other threonine and a serine) which + - might accommodate a phosphate. I have tried to fit a number of molecules, e.g., the substrate (but not really good in all monomers for the phosphate moiety), glycerol, ethylene glycol and its di and tri (found also in other places in the structure) and now I went for glyceraldehyde (though, I have doubts that there is other - apart from the one eventually bound to S - tertiary carbon). Apart from the difficulties on searching for the best fitting molecule (and consider their intrinsic flexibility) I do not manage to establish distance between them and Cys SD (and there goes the second question). 2) I could not devise how to set a proper distance between any of the ligands and the Cysteine, be it to check for a covalent bond or to establish a van der Waals restriction. I tried: bond { action = *add delete change atom_selection_1 = chain A and resid 153 and name SG atom_selection_2 = chain N and resid 5 and name C3 symmetry_operation = None distance_ideal = 1.803 sigma = 0.1 slack = None limit = -1.0 top_out = False } Results are also show for my Glyceraldehyde trial, last 4 photos, https://photos.google.com/album/AF1QipO71L7GJYKv_MmjTc_0GzsH2xtFR_V-2ICBirPb . Note clashes. Curiously , for some of the bonds to be added, I receive the message: " Atom "HETATM 9835 O2 3GR N 5 .*. O " rejected from bonding due to valence issues." which seems to point to oxygen atoms, though I declare carbon atoms. Helps welcome, thank you. Jorge

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mr_rosetta build test
by Wei Wang 17 Jul '20

17 Jul '20

Dear all, I would like to ask a question about the testing of mr_rosetta build. Is the “phenix_regression.wizards.test_command_line_rosetta_quick" still available? I checked my early build on Mac it is there, but that build was ~3 years ago. However on a recent build on Ubuntu 18.04 the option is not available (I ran the rosetta.run_tests and it’s ok though). Regards, Wei

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occupancy_sum_constraints
by Petros Giastas 15 Jul '20

15 Jul '20

Dear all, I have a metal compound interacting with a protein and I am facing the following problem. Initially, the metal is equatorially complexed with chlorides, which are progressively exchanged by water molecules. This hydrolysis is clear from our spectroscopic analysis, but also from the anomalous maps, which show weaker peaks for the most exposed chlorides. The question regarding phenix.refine is: How can I refine the occupancies of the alternative species (chlorides and water molecules) and to constrain their sum into the occupancy of the metal, which is also under refinement? I cannot find the proper selection syntax to deal with this situation. Can you help me on that? Thank you in advance. Petros P.S. I remember I could treat this kind of problem with shelxl but it has been a lot of time since I last used shelxl for high resolution protein refinement and I would not like to go back.

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PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
by Bjørn Panyella Pedersen 13 Jul '20

13 Jul '20

Dear colleagues, We have a open PhD position my my group. Please pass along to anyone who might be interested. Thanks! Deadline is July 31st. /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn 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. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). 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. Deadline is July 31st. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk).

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phenix writing files with wrong job number
by Green, Todd Jason 09 Jul '20

09 Jul '20

Hello All- Phenix has started to write files from each job with incorrect job number notation. It puts them into the correct directory (ie. with correct job number, ex. Refine_23) but with file names having wrong job number (ie. where they are job number - 1, ex. protein_refine_22.pdb). This causes issues with the gui. I can edit the names post run, but is there a permanent fix. Just start a new project? Probably upgrade to the new version is the first choice. FYI I'm running 1.17.1-3660-000 on a macbook. Seems to have just started spontaneously. Thanks for the help- Todd

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The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine
by Zixian Li 08 Jul '20

08 Jul '20

Dear Phenix Community, I'm at beginner level of using Phenix. I have difficulty to refine a protein-RNA complex in Phenix. I refined the protein model without RNA first, then I built the RNA model into the difference density map in Coot through Calculate>Other Modelling Tools>Ideal DNA/RNA, where I input the sequence and fit nucleotides into the density. At the 5' end it's guanosine triphosphate (GTP) but the modeler tool in Coot only generates nucleoside monophosphate. So I built the RNA model from the second nucleotide at 5' end downstream until where RNA density was too poor to model. I did the real space refine zone in Coot to fit this main part of the RNA into its density the best possibly. For the GTP at 5' end, I realized there is GTP.cif restraint file in Phenix monomer library. So I obtained an arbitrary pdb file for GTP using eLBOW and corrected atom names matching the definition in GTP.cif file. Then I can also fit GTP into the RNA density at 5' end using real space refine zone in Coot. Now I have a broken RNA model with GTP unlinked to the ribose-phosphate backbone. For Phenix refinement, I supplied a cif_link_GTP-G.params file to define the linkage for the two RNA chains in the complex: refinement.pdb_interpretation { apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } } After refinement, I noticed O3' of GTP appears connected to P of the following nucleotide G in the refined model in Coot. However, if I do the real space refine zone in Coot, the linkage becomes broken, i.e., I cannot refine the RNA model as a whole: Coot only allows separate real space refine for GTP and the rest. It seems Coot still cannot recognize GTP and the rest as one body. In the refinement settings there is a button for Automatic linking options. Interestingly, I noticed if I leave the automatic covalent linking as default, Phenix writes Link records in the output pdb after refinement. But it also links one of the protein residues to the GTP in chain D. In order to avoid the unwanted intermolecular linkage, I clicked Link none for Automatic linking options, then there is no any link records written in the output pdb despite of the defined linkage in cif_link_GTP-G.params file. So it seems for me Phenix ignores the input cif_link_GTP-G.params file, it writes Link records only if the Automatic linking option is activated. I worried whether it could be due to the syntax of the cif_link_GTP-G.params file. So I tried the following syntax in two separate files, the same issue was observed. cif_link_GTP-G_chC.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } cif_link_GTP-G_chD.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } I also need to point out that p linkage is pre-defined in the list of links (mon_lib_list.cif) in Phenix monomer library. I apologize for this long explanation of the problem. I hope it is clear. I really appreciate your advice in advance. Sincerely, Zixian Li

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Heteroatoms addition to crystal structures
by Shirin Akbar 06 Jul '20

06 Jul '20

Dear all, I am using the phenix.real_space_refine program for refinement of crystal structure in cryo-EM map (ribosome map, 3.4 A resolution). Prior to real_space_refinement I had removed all the heteroatoms. What is the correct way to add the cations (eg. Mg2+ ions) to the structure and how do I do it? Can anyone kindly suggest.. Thanks & Regards Shirin -- *Shirin Akbar*

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real-space refinement resolution
by Alexei Gorelik 29 Jun '20

29 Jun '20

Hi, When refining a model against a density-modified cryo-EM map, should one use the resolution of the original or modified map? Thanks

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Refining cytochrome structure with hemes
by Yangqi Gu 29 Jun '20

29 Jun '20

Dear Phenix developers. I have a simple question regarding the real space refinement. I am working on a cytochrome structure and I would like to know how to refine the model with hemes present against the map? Also, how do I create vinyl bonds at my cysteine positions to connect the hemes? More ideally, could I refine the heme geometry as well? Thank you in advance! Best, Yangqi

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CryoEM Post-Doctoral Position
by Hasan, Syed Saif 25 Jun '20

25 Jun '20

Interested in exploring the world of molecular espionage? Want to find out how viruses hitchhike between organelles during assembly? Join my lab as a post-doctoral researcher to decipher the secret life of epidemic causing viruses at the atomic scale. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses such as Dengue, SARS-CoV-2, and pox viruses take over host membranes during intra-cellular progeny assembly. We are located in Rockville MD in the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan), which is 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 keV Talos Arctica with a Falcon 3EC DED and a 200 keV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. If you are interested, send me your CV. Lets talk. ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Energy minimization and explicit solvent model
by Andre LB Ambrosio 24 Jun '20

24 Jun '20

Dear colleagues, could you please suggest a computational tool to perform energy minimization of a crystal structure under explicit solvent conditions (i.e, types and concentrations of ions, pH)? I want to observe the solvent effects on the conformational space around a starting model, all-atom, while preserving its geometry (I guess it can be better expressed as relaxation). Thank you in advance. -- Andre LB Ambrosio

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Senior Scientist Position at AbbVie
by Jain, Rinku 24 Jun '20

24 Jun '20

Hi Everyone, I would like to draw your attention to the following job opportunity at AbbVie: Senior Scientist I, Protein X-ray Crystallography https://careers.abbvie.com/abbvie/jobs/2004610?lang=en-us&previousLocale=en… The Protein Crystallography Group at AbbVie (Illinois, USA) is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern X-ray Crystallography techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Scientist will utilize fragment-based strategies to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. To learn more about AbbVie, please visit: https://www.abbvie.com/ Best, Rinku --------------------------------------------------------------------------------------------------------------------------------------------------- Rinku Jain, Ph.D. Senior Scientist II, Structural Biology [cid:[email protected]] I AbbVie, Inc. 1N. Waukegan Road, AP10-LL North Chicago, IL 60064-6098 EMAIL rinku.jain(a)abbvie.com<mailto:[email protected]>

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13th CCP4/APS Crystallographic School in the US
by Xu, Qingping 24 Jun '20

24 Jun '20

Dear Colleagues, We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php. Dates: June 15 through 22, 2020 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1th, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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No NCS restrains in phenix.real_space_refine?
by Aaron Oakley 21 Jun '20

21 Jun '20

Am I correct in saying that phenix.real_space_refine does not (yet?) have NCS restraints (that I need for refining a molecule with broken symmetry)? With thanks, –å

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Water molecules whose existence is contingent on the alt conf of a side chain are deleted in refinement
by Dale Tronrud 17 Jun '20

17 Jun '20

Hi, I have a model with a Tyr side chain with two conformations. When it is in the A conformation three water molecules occupy the site of the B conformation. I have defined these water molecules to have the alt loc A (with no B versions) and set their occupancy equal to that of the A version of the Tyr. During refinement, using the GUI, these water molecules disappear during the "add/remove water" stage. My guess is they are running afoul of dist_sol_mol_min. I can't find where I can set this parameter to some, very small, value that will allow these waters to live and prosper. If this is my problem, how can I disable this check? Dale Tronrud

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PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
by Bjørn Panyella Pedersen 15 Jun '20

15 Jun '20

Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn ============================================ STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn 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. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). 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. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk). 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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Web server update
by Billy Poon 14 Jun '20

14 Jun '20

Hi everyone, The software running phenix-online.org has been updated. Please let us know if you experience any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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ACA 70th Annual Meeting: August 2-7, 2020 - Abstract Deadline Monday 6/15!
by Lisa J. Keefe 12 Jun '20

12 Jun '20

<http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> The deadline to submit an abstract for an oral presentation is Monday, June 15, 2020! Submit An Abstract Today! <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> “Training the Next Generation” <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> 1.1.4 & 1.2.2 Microcrystal Electron Diffraction (MicroED) – Small Molecule & Macromolecules 1.2.3 Communicating Science to the Public 1.2.5 In situ / operando: From Synthesis to Devices 1.2.4 Advances in Fiber Diffraction 2.1.4 Frontiers in SAS 2.3.1 Would You Publish This? 1.2.1 Remote Access Facilities: What, Where & How? 2.1.2 Advances in Software Methods and Tools for Cryo-EM 3.2.3 Structural Contributions to SARS-CoV2 and the COVID-19 Pandemic T1&2 Structural Science: New Ways to Teach the Next Generation 4.1.2 Structural Dynamics I. Protein Collective Motions Studied by X-ray Scattering and Diffraction 4.2.4 Physics and Chemistry of Matter Under Extreme Conditions 3.1.1 CryoEM in Pharma: Structure-based drug design beyond X-ray crystallography 4.2.2 Structural Dynamics II. Conformational Ensembles of Proteins Studied by Cryo-EM and X-ray Scattering 2.2.3 & 4.2.3 General Interest 3.1.4 & 3.2.4 Cool Structures: Important Science from Small Molecules 4.1.1 Methods and Tools for Crystallography and Cryo-EM Sample Preparation 3.2.3 Hot Structures *** There is no fee to submit an abstract, but you must be an ACA member to submit an abstract or attend the meeting. Join or renew today! <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> For more information and to register to attend the meeting, visit our conference website at www.acameeting.com <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…>. -The American Crystallographic Association- <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…>

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phenix eLBOW and phosphorous stereochemistry
by Xavier Brazzolotto 11 Jun '20

11 Jun '20

Dear all, I use phenix.elbow in order to generate mol2 files that will then be used in a docking process through autodock/vina. I am facing a strange issue. While using a SMILES string bearing stereochemistry at a desired phosphorous atom as eLBOW input file, the correct stereochemistry is not respected in the output files. While giving PR or PR compound, I always end up with the very same enantiomer… Maybe eLBOW does not handle the phosphorous specific stereochemistry ? Many thanks Xavier Brazzolotto, PhD

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SSBOND for protein-ligand
by Wei Wang 09 Jun '20

09 Jun '20

Dear all, I’m seeking help for establishing disulfide bond between protein and ligand. I used phenix.readyset to prepare the model for refinement then used phenix.elbow to generate the cif for ligand. After refinement, the sulfur from ligand, which was meant to be forming disulfide bond, is linked to the adjacent CYS by dashed line. I do see the LINK record in refined pdb. I tried manually add SSBOND record line in the pdb, following format instructions on wwpdb, but didn’t succeed. Thus I’m here looking for help on how to properly introduce disulfide bond between a ligand and cysteine. Some further explanation: When I display the readyset output in Pymol, the disulfide bond seems to be correctly recognized. I guess it’s because the sulfur atoms are within the detectable distance for a SSBOND. When I opened the same pdb in Coot, the disulfide bond is not present. I noticed a similar situation in PDB:6O9V, where the ligand M1M (chain B and resseq 401) was refined with LINK record but not SSBOND. (Sorry if this is a repeat message: previous message was put on hold because attachment pic size was too big.) Regards, Wei

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Phasing@Home event
by Claudia Millán Nebot 05 Jun '20

05 Jun '20

Dear PhenixBb community, We are glad to announce the first Phasing@Home event, an online meeting devoted to presenting XDS, ARCIMBOLDO, Phaser and SHELX software and their use in challenging phasing cases. Confirmed speakers and members of the teams: Institut de Biologia Molecular de Barcelona (IBMB-CSIC): Isabel Usón, Claudia Millán, Ana Medina, Iracema Caballero, Elisabet Jimenez, Albert Castellví, Giovanna Petrillo, Josep Triviño Cambridge Institute for Medical Research (CIMR): Randy Read, Airlie McCoy, Rob Oeffner, Kaushik Hatti, Massimo Sammito, Tristan Croll University of Konstanz: Kay Diederichs University of Goettingen: George Sheldrick Instituto de Biociencias, Universidade Estadual Paulista (UNESP): Rafael Borges The full schedule can be found under: http://chango.ibmb.csic.es/phasingathome The meeting will hosted via Zoom and is free of charge but you will need to pre-register here: https://www.eventbrite.co.uk/e/phasinghome-tickets-107673520398 The event will be held online on the 13th and 14th of July. Talks will be short and focused on covering the advanced usage of the software, so participants are expected to be familiar with the basics already or to browse some basic material provided by us in advance. Interaction among speakers and participants will be through a Discord (https://discord.com/) server. Please note that this event is limited to 25 external participants and provided they meet the requirements of presenting some challenging dataset, the acceptance upon registration will be on a first-come, first-served basis. With best wishes, ---------------------------------------------------------------------------------------- Claudia Millán (cmncri(a)ibmb.csic.es) Crystallographic Methods Group http://chango.ibmb.csic.es Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain LinkedIn: es.linkedin.com/in/claudiamillan/ <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> ResearchGate: https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf Twitter: https://twitter.com/cheshireminima and Massimo Sammito

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Amber module in phenix on Ubuntu 18.04
by Guenter Fritz 04 Jun '20

04 Jun '20

Dear all, dear Nigel, I cannot get the Amber and AFITT menu bars in the phenix.refine GUI on a Ubuntu (Xubuntu 18.04) box. I set Preferences "Enable alpha-test programs and features" (works on my Mac 10.14.6 and SciLinux6 box ). Moreover, on the Xubuntu machine: when I start the phenix.refine GUI (phenix version 1.18.2-3874) I see the following error message in the terminal running phenix: //$ phenix// /Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh / //------------------------// python 3.7 is installed and python development tools :/ / /------------------------ / /$ python -V // //Python 3.7.6 / /$ sudo apt list -a python3.7-dev // //Listing... Done // //python3.7-dev/bionic-updates,now 3.7.5-2~18.04 amd64 [installed] // //python3.7-dev/bionic-security 3.7.3-2~18.04.1 amd64 // //python3.7-dev/bionic 3.7.0~b3-1 amd64 / /------------------------/ Any idea what is going wrong? Thanks a lot and best regards, Guenter

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Post-doctoral position in Neutron/X-ray crystallography at the Institut Laue Langevin (Grenoble, FR)
by Nicolas Coquelle 03 Jun '20

03 Jun '20

Dear all, The Large Scale Structure group of the Institut Laue Langevin (Grenoble, FR), in collaboration with the group of Elspeth Garman (Oxford, UK) has an open position for a post-doctoral fellow in neutron/X-ray crystallography to study radiation-damage. Please see the description below and contact me (coquelleni(a)ill.fr <mailto:[email protected]>) for further information. Best regards, Nicolas Coquelle.

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Imposing bond restraints across the asymmetric unit
by Brandon J Anson 27 May '20

27 May '20

Hello, I have an unusual problem in which my enzyme (a dimer) is covalently bound to its own C-terminus and so is daisy-chained across the crystal lattice. In the past, I have encountered and fixed this problem by extracting the covalent part of the molecule and re-phasing using that as the molecular replacement model. In this case, I am not able to due so. When I input the restraints, it either crashes refine or attempts to impose them on the corresponding residues within the ASU (understandable) but they are quite distal and this leads to "interesting" refinement results. Is there a good way of making phenix.refine do what I want? Or perhaps a workaround that I haven't considered yet? Best Regards, Brandon

3 2

Refinement problem in phenix
by Muhammad Bashir Khan 22 May '20

22 May '20

Hi there; I find some unknown density in my map, where I put SO4 and in some UNX. I merged and save all in one PDB. I run ReadySet to make cif. file, but refinement still not working. Can anybody explain what else I should provide? Thanks in advance Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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symmetry conflicts
by Daniel Larsson 22 May '20

22 May '20

I want to report an annoying bug in version 1.18.2-3874. My real_space_refine job ended with an error at the validation step saying Crystal symmetry mismatch between different files. This was when refining a PDB structure (first processed using ready_set) in a cryo-EM map. The “Ignore symmetry conflicts” checkbox was checked. The expected output files were generated, but no validation report was generated. Regards, Daniel 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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byron bender
by Taufiq El-Mokdad 22 May '20

22 May '20

Hi all, I am a student from Halle in Germany. I really want to try out doing a wire model for proteins with the Byron Bending machine, yet I couldn’t find out where to get one and the Charles Supper Company discontinued selling these devices. I was recommended asking here for help. Is there anybody still having one of these devices in their labs or having one starting to rust in a box in the attic? I would be really statisfied trying out making some wire protein models with it. If someone would be willing to give such a machine and I would of course pay the shipping costs I would be happy to hear about. I would also be grateful if someone could give me a tip where I could still ask? Thanks.. All the best Taufiq

1 0

Alternative conformation on special position occupancy wrong
by Kaiser, Jens T. 20 May '20

20 May '20

Hi, We have a case of a cofactor with 222 symmetry in two states on a special position ( 2-fold). When modelling one state, Phenix correctly restrains the occupancy to 0.5. When putting state 2 in alternative conformation group B, the occupancy of altconf A and B is restrained to 1.0, instead of 0.5; it seems like it does not recognize that the alternative conformations are on a special position. Cheers, Jens Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Phenix version 1.18 released
by Paul Adams 20 May '20

20 May '20

The Phenix developers are pleased to announce that version 1.18 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.18.2 version of Phenix: 1.18.2 Changes - Fix weighting for iron sulfur clusters 1.18.1 Changes - General bug fixes 1.18 Changes - Amber - Automatic creation of Amber files in phenix.refine GUI - Added AmberPrep GUI - Restraints - Engh & Huber restraints (2001) for cis-peptides now implemented - Restraints added for FeS - Metal coordination library is default to Zn+2 and FeS clusters - Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). - Density modification for cryo-EM - Includes model-based density modification with automatic model generation - Optimized defaults and additional documentation - Real-space refinement - Hydrogen atoms no longer included in map target function, which improves fit. - Add NQH flip option (enabled by default) - Other - New tool for ordered solvent picking in cryo-EM maps (phenix.douse) - New map and model superposition tool (phenix.match_maps) - New FindProgram to find any Phenix program with a text search - Project details now has a button for opening the README file for tutorials For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Generating a polder map using coordinates
by Petr Kolenko 20 May '20

20 May '20

Dear colleagues, Is there a way to calculate the polder map in a selected box using coordinates instead of atom selection as shown in the "Generating a polder map with the compute_box option" website? Best regards, Petr

3 2

Solving a protein - ligand structure
by Tom Vanmarcke 20 May '20

20 May '20

Dear, We are trying to solve a protein structure that contains a ligand (polyoxometalate). We found the ligand in the electron density but through the middle of the ligand goes a 2 fold axis. For this reason, we placed the occupendency of the ligand on 0.50. When we try to refine the structure using phenix.refine, the ligand breaks down even when adding a cif restrain file. The cif restrain file contains information about atoms, angles and bond lengths. Is there a way to fix this problem? Greetings Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Is there a way to evaluate batch pdb models with Malprobity in phenix?
by Jing Liu 18 May '20

18 May '20

Hi, I had generate a batch of pdb models (40-100) in rosetta and am wondering whether there is a way to evaluate these models in batch with Molprobity. For example, can I use phenix command line to do it and how? Or should I download the Molprobity and do it on my local computer? Really appreciate if anyone can share their experience. Jing Liu, PhD Ted Jardetzky lab Department of Structural Biology Stanford University

2 3

Phenix 1.18 and rotamer outliers
by Xavier Brazzolotto 18 May '20

18 May '20

I’ve installed the latest stable Phenix version (1.18). I’ve noticed a clear difference in the final statistics (MOLprobity) compared to the previous version (1.17). A bit more of Rama outliers and the most noticeable in the Rotamer outlier score. Is there any reason that could explain such behaviour ? I am using Phenix under MacOS. Xavier Brazzolotto, PhD xavier.brazzolotto(a)chemdef.fr Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy.

2 1

unit cell dimesions
by Thomas, Leonard M. 13 May '20

13 May '20

Hello All, I have run into something that has me a bit puzzled. When finishing up a structure we ended reprocessing the data to get nice statistics for deposition, I don’t want to get into that discussion. Upon reprocessing the unit cell dimensions shifted slightly, 0.05 A or so. The PDB file used had the unit cell from the original solution/refinement while the data set cell dimensions were different. I ran the newly processed reflection data set through the reflection editor in order to transfer the Rfree set. Now the really odd thing is that I ended up reprocessing a couple times and transferring over the Rfree set once more. The cell dimensions on the final reflection file is from not the original reflection file/PDB but one that was used with an intermediate cutoff between the two, it is not the cell dimensions in the input reflection either. Just for completeness the data were processed using XDS at SSRL. My question is where does phenix.refine pick up the unit cell dimensions and were does the reflection file editor pick them up? Best Regards Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

2 1

install fail in linux
by 안우찬 12 May '20

12 May '20

Hi, I have a problem with install phenix-1.18.1-3865 in linux. My linux version is NAME="Red Hat Enterprise Linux Atomic Host" VERSION="7.4.0.4". The error massage is ============================================================================= Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 190, in install self.check_directories() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 268, in check_directories os.makedirs(i) File "/usr/lib64/python2.7/os.py", line 157, in makedirs mkdir(name, mode) ============================================================================= Thanks in advance, Teddy Ahn

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How to compare between electron density maps?
by Murpholino Peligro 11 May '20

11 May '20

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

4 3