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Runtime error : Bond distance
by Luca Pellegrini 06 Sep '22

06 Sep '22

Phenix real space refine (dev 4704) crashes with: RuntimeError : Bond distance > max_reasonable_bond_distance: 67.4676 > 50: I’ve found various reports of this error in the bb but no (to me) clear solution, only one suggestion to increase the max_reasonable_bond_distance (Nov 2017). I tried setting excessive_bond_distance_limit (I guess is the same) to 999 but with no success as Phenix stops with the same error. Any help on how to fix this gratefully received. Best wishes, Luca

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Reference model restraints
by Luca Pellegrini 01 Sep '22

01 Sep '22

Hello, Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at https://phenix-online.org/documentation/reference/real_space_refine.html#us… phenix.real_space_refine model.pdb map.mtz \ reference_coordinate_restraints.enabled=true \ reference_coordinate_restraints.selection="chain A and resseq 12:21" \ reference_coordinate_restraints.sigma=0.05 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Phenix website downtime
by Billy Poon 01 Sep '22

01 Sep '22

Hi everyone, There was some networking issue which caused the Phenix website to be down for several hours. The site should be back to normal, but please let us know if you have 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 Fax: (510) 486-5909 Web: https://phenix-online.org

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RNA structural biology position (Scientist-Sr.Scientist) at Arrakis Therapeutics
by Elena Menichelli 25 Aug '22

25 Aug '22

Dear all, We have an open position for an RNA structural biologist at Arrakis Therapeutics (Boston, MA area). The ideal candidate will have a background in structural characterization of RNA (X-ray crystallography, cryo-EM or atomic force microscopy) and a passion for developing small molecules that target RNA in a very collaborative environment. Please feel free to visit Arrakis’ website for a more detailed job description and to reach out to me for additional information and informal discussion. https://arrakistx.com/careers/current-openings/ With best regards, Elena ******* Elena Menichelli, PhD | Head of Structural Biology emenichelli(a)arrakistx.com<mailto:[email protected]> | www.arrakistx.com<http://www.arrakistx.com/>

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Launch of IUCrData Raw Data Letters: Editorial
by John R Helliwell 24 Aug '22

24 Aug '22

Dear Colleagues, I imagine you will be interested to know of the launch of IUCrData’s Raw Data Letters. The Main Editor is Dr Loes Kroon Batenburg. See https://forums.iucr.org/viewtopic.php?f=39&t=449&p=729#p729 Greetings, John Emeritus Professor John R Helliwell DSc Chair of IUCr CommDat

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phenix.refine command lane xyz restrains
by Błażej Bagiński 24 Aug '22

24 Aug '22

Dear Phenix community, lately I started toying with the terminal version of our favourite refinement software (on kubuntu linux). I'm refining a structure with a ligand that is not in the refmac database (.cif file needed), and I couldn't find anything on how to implement xyz coordinates restraints for the procedure. In other words, I have a ligand that I built into the polder map and I want to tell the software "do not change the positions in space of these atoms". How can I do that? Also, side question: why there are three different(?) versions of command line phenix.refine for every phenix installation? What is the difference between them? REMARK 6 I followed the online guide for "Refinement at high resolution" on my 1,2~1,3A structure and the results were surprisingly nice, I'd say potentially even better than usually used parameters in GUI (5 cycles both). Kind regards, Blazej

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Postdoctoral Research Associate in the Structural Biology of Supramolecular Protein Assemblies
by Owen Davies 19 Aug '22

19 Aug '22

Dear all, I would like to advertise a postdoctoral position that is currently available in my lab at the Wellcome Centre for Cell Biology, University of Edinburgh, UK (https://www.wcb.ed.ac.uk/research/owen-davies). This position is for an initial period of three years (with possibility to extend), to work on the integrative structural biology of the synaptonemal complex. The synaptonemal complex is a supramolecular protein structure that assembles during meiosis to facilitate homologous chromosome synapsis and crossover formation. Its immense structure, of many micrometers in length, is formed through the combination of at least three unique self-assembling protein systems, which individually form lattice-like arrays, para-crystalline filaments and 'intermediate filament'-like fibres. This position aims to determine the molecular structure of the human synaptonemal complex and its constituent complexes through their reconstitution from recombinant proteins. This will be achieved through a cutting-edge structural biology approach, involving cryo-EM single particle reconstruction and tomography, structure solution of components by X-ray crystallography, solution biophysics (including X-ray and light scattering, and single-molecule biophysics), and the integration of experimental findings by advanced computational modelling of structures and assembly dynamics. The post is funded by a Wellcome Senior Research Fellowship, and will be hosted in a well-equipped and well-funded lab, which includes the following: Extensive biochemical equipment (including numerous Akta Pure systems, SEC-MALS etc) Protein production and characterisation facility (https://www.ed.ac.uk/biology/research/facilities/edinburgh-protein-producti…) State-of-the-art biophysics equipment (including C-trap optical tweezers) In-house TEM, SEM and newly upgraded cryo-EM facility (https://www.ed.ac.uk/biology/research/facilities/electron-microscopy) Regular time on macromolecular crystallography and SAXS synchrotron beamlines at Diamond Light Source (https://www.diamond.ac.uk) Regular cryo-EM time on Titan-Krios microscopes at Diamond Light Source (https://www.diamond.ac.uk) and Jeol microscopes at the Scottish Centre for Macromolecular Imaging (https://www.gla.ac.uk/researchinstitutes/iii/cvr/facilities/scmi/) Local provision of high-performance GPU computation for cryo-EM, modelling and molecular dynamics This position provides a unique opportunity for a highly enthusiastic applicant to perform transformative research through an integrative approach that is directed towards the new era of structural biology that address protein assemblies at a cellular scale. The successful candidate will lead this project (including several PhD students), and will be fully supported in applying for postdoctoral research fellowships within the lab, and independent research positions at the end of the postdoc. In suitable cases, at least part of the project, or a new project to be started during the employment, could be taken by the successful candidate as the basis for their future research career. Please see the following manuscripts for examples of our previous work: https://www.nature.com/articles/s41594-021-00636-z https://www.nature.com/articles/s41594-018-0078-9 https://www.nature.com/articles/s41467-018-07794-7 https://www.science.org/doi/10.1126/sciadv.abb1660 https://elifesciences.org/articles/60175 Full publication list available at https://www.ed.ac.uk/profile/dr-owen-davies The advert for the position is available via the following link: https://www.jobs.ac.uk/job/CRX346/postdoctoral-research-associate-in-the-st… The application deadline is 6th September, and candidates should apply by following the 'apply' link on the above advert. Please feel free to contact me directly (Owen.Davies(a)ed.ac.uk<mailto:[email protected]>) for informal discussions and additional information. Best wishes, Owen. Dr Owen Davies Wellcome Senior Research Fellow Wellcome Centre for Cell Biology University of Edinburgh Michael Swann Building Max Born Crescent Edinburgh EH9 3BF United Kingdom The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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Inability to connect the N and C terminal of peptide to form a peptid bond of a circular peptide structure
by Jiang Xu 14 Aug '22

14 Aug '22

Hello Guys, I have a circular peptide structure solved from Xtal. The peptide is actually a circular peptide that has the N terminal and C terminal joined together by a peptide bond. When refining the structure, I had a problem getting the C-N terminal (between G34 and S2) joined together by the peptide bond. I even made a link between the C terminal carbon atom and N terminal N atom in coot and used this model as the input model to do the refinement using Phenix.refine. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoid forming a bond between the C atom and the N atom. So, how can I solve this problem? Thank you, Best regards, Jiang Lin Chen Lab University of Southern California P.S. coot manually made link between the C and N terminal [image: unnamed.jpg] After refinement [image: unnamed (1).jpg]

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Postdoc Opportunity - Multidataset X-ray Crystallography, Computational Structural Biology, & Protein Allostery - Upper Manhattan, New York City
by Keedy, Daniel 09 Aug '22

09 Aug '22

Hello Phenix community, The Keedy Lab at the CUNY Advanced Science Research Center in New York City has a funded Postdoctoral Scholar position available immediately. We seek applications from individuals with experience in computational biology, computer science, software development, biochemistry, biophysics, or a related area. Details of research projects and career training will be tailored to the goals of the successful applicant. Research: The Keedy Lab is interested in the interplay between protein sequence, conformational heterogeneity, and biological function. Using a unique combination of avant-garde computational and biophysical approaches, we aim to elucidate the conformational ensembles of proteins and to understand how they are shifted by perturbations, including temperature, pressure, mutations, ligands, protein:protein interactions, to control biological function. The successful applicant for this open position will join these efforts by developing and using new computational approaches to exploit families of related structures, extract hidden signatures of conformational heterogeneity, and explore how changes to amino acid sequence rewire protein allosteric networks. Location: The CUNY Advanced Science Research Center (https://asrc.gc.cuny.edu) is a cutting-edge research institution, perched atop a hill overlooking Harlem in New York City. Alongside its sister research building, the City College of New York’s Center for Discovery and Innovation, the ASRC sits in an oasis of green amidst upper Manhattan. The ASRC Structural Biology Initiative features eight tenure-track and research-track faculty members, pursuing diverse research problems using X-ray diffraction, mass spectrometry, cryo-EM, NMR, solution biophysics, and advanced microscopy. The ASRC is immediately adjacent to the New York Structural Biology Center, a consortium of CUNY and eight other New York academic institutions with world-class facilities, and is just 70 miles from Brookhaven National Laboratory, featuring the National Synchrotron Light Source II – the brightest synchrotron light source in the United States. You can read more about the Keedy lab here: https://keedylab.org Please officially apply for the position here: https://www.rfcuny.org/careers/postings?pvnID=RC-2207-004956 You may also email me directly to ask questions or discuss. I look forward to hearing from you! Best regards, Daniel Keedy — Daniel A. Keedy, PhD Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry, Biology, and Chemistry PhD Programs, CUNY Graduate Center dkeedy(a)gc.cuny.edu<mailto:[email protected]> | https://keedylab.org | 919-724-6064

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Naming/refining glycosylation
by Tynan Young 09 Aug '22

09 Aug '22

Hi all, I am having issues with naming of glyco- groups and refining my glycosylated EM structure in Coot. I have noticed that many models use the same chain ID for the glyco- groups as the chain ID they are attached to (i.e. NAG/B/1301 would be linked to ASN/B/121). When working with the model in Coot, I would like to refine only the ASN 121 and the NAG 1301 attached to it. However, due to the naming of the glyco- group, Coot will refine residues 121-1301. Not only is this very time-consuming, but it will disrupt the rest of the model - which I do not want to do. If I change the chain ID of the glyco- group to an altogether different chain ID, then I can no longer refine both the side chain and the glyco- group. Is there some naming scheme that avoids this issue? Any help is greatly appreciated. Thank you. Tynan ---------------------------------------------------------------------- ------------------------------------------------------------ -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ------------------------------------------------------------

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