- phenixbb - phenix-online.org

Re: [phenixbb] [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
by David Briggs 22 Jun '21

22 Jun '21

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

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Macromolecular Crystallography School 2021
by Nicole Larrieux 21 Jun '21

21 Jun '21

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

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Phenix.real_space_refine crash
by Reza Khayat 18 Jun '21

18 Jun '21

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

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

16 Jun '21

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

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

16 Jun '21

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

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

15 Jun '21

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

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C-C sugar linkage in real-space refinement
by Kevin Jude 15 Jun '21

15 Jun '21

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

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Turn off side chain optimizations in phenix real space refine?
by Oliver Clarke 11 Jun '21

11 Jun '21

Hi, Is there any way to turn off rotamer fitting/side chain optimization in phenix.real_space_refine? Sometimes it seems to do more harm than good, and repositions sidechains completely out of the density, but I couldn't find how to switch it off. Cheers Oli

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General interest: the history of the European Crystallography Schools
by John R Helliwell 11 Jun '21

11 Jun '21

Dear Colleagues, Th history of the European Crystallography Schools, initiated by Italian colleagues (ECS1 was held in Pavia), is described here at the ECA’s website:- https://ecanews.org/european-crystallography-school/ Several of these previous Schools’ details, but not all as yet, can be found here:- https://ecsx.ecanews.org/ ie replacing the x by the number. The current one ‘Budapest’ being 6. (In each the ECA website is mirrored to the local host organising team.) Greetings, John Emeritus Professor John R Helliwell DSc ECA Past President 2007 to 2010

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European Crystallography School ECS6
by John R Helliwell 10 Jun '21

10 Jun '21

Dear Colleagues, I commend to you the European Crystallography School ECS6. Full details are here:- https://akcongress.com/ecs6/ Best wishes, John Emeritus Professor John R Helliwell DSc

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Restraints for small molecules in macromolecular crystal structures
by Marie Elizabeth Fraser 10 Jun '21

10 Jun '21

Hello, The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement. What do others do? As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX? The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints. Thank you, Marie

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Associate Researcher Position in the KU Protein Structure Laboratory
by Lovell, Scott W 08 Jun '21

08 Jun '21

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is seeking a full-time Associate Researcher to assist with various structural biology projects. As a core laboratory, the PSL collaborates with a diverse range of investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSL manages the structural biology efforts for extramurally funded research projects particularly aimed at inhibitor development. For a full description of the position and to apply, GO TO: https://employment.ku.edu/associate-researcher/19212br Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 __________________________________________________

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Postdoctoral Scholarship Opportunity in the Lane group (PBIO) CFEL/DESY, Hamburg, Germany
by TJ Lane 08 Jun '21

08 Jun '21

Uncovering protein dynamics: developing statistical crystallography Postdoctoral Scholarship Cluster of Excellence: Advanced Imaging of Matter Center for Free Electron Laser Science (CFEL), Hamburg, Germany Protein motion is at the heart of life, but remains challenging to witness firsthand. Proteins move to reading and copying DNA, convert sunlight into chemical energy, and transmit signals between cells, yet our ability to image these functions is limited by the technology we have to image protein dynamics. A new opportunity to meet this challenge is emerging, however, as crystallographic methods advance. We can now collect data from thousands to millions of crystals of the same protein, and it is clear no two crystals are identical. Thus, analyzing their distribution may reveal protein structural fluctuations directly. Can we develop a statistical crystallography to turn these large datasets into knowledge about protein dynamics? Can we use statistical analysis of crystal-to-crystal variation to separate signal from noise in time resolved experiments, revealing protein motion induced by mixing with a ligand or excitation with a pump laser? We seek a computational scientist who will answer these questions. As the ideal candidate, you will have the following key attributes: * A doctoral degree in physics, biophysics, chemistry, applied mathematics or a related field * Working knowledge of macromolecular crystallographic methods and software * A track record of scientific computing and programming * The ability to drive your work independently and show initiative And you will be excited to take on the following responsibilities: * Mathematical modeling of protein dynamics and protein crystal diffraction data * Interpretation and analysis of experimental results * Open-source development to make your insights available to the broader scientific community * Presenting your work in written and oral form to the scientific community * Helping to foster an environment conductive to collaboration, learning, growth, and fun Available immediately is a two-year contract with a competitive salary and the opportunity to work and live in the beautiful and vibrant city of Hamburg, Germany. The group is housed at the Center for Free Electron Laser Science on the vibrant DESY campus (Luruper Chaussee 149, 22761 Hamburg, Germany). This position is funded through the Advanced Imaging of Matter Cluster of Excellence (https://www.cui-advanced.uni-hamburg.de/en.html). The successful candidate will become a fellow of the cluster and have access to career support, training opportunities, and an engaging scientific network via the cluster. The candidate will have additional technical and mentorship support from partners Andrea Thorne, Arwen Pearson, and Nicholas Pearce and their groups during the course of the project. We are an equal opportunity employer. Women and minorities are encouraged to apply and handicapped persons will be preferred given equal qualifications. Application deadline: 17 June 2021 Applications should include a cover letter, a tabular curriculum vitae, and copies of degree certificate(s). Please send applications by email to: < thomas.lane(a)desy.de> For more details, write directly to TJ Lane: <thomas.lane(a)desy.de> Cross-Posting on the AIM Cluster of Excellence page (funding source for this project): https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=4c3ff9d…

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Quick calculation of mean ADP
by Martin Malý 07 Jun '21

07 Jun '21

Dear mailing list members, I would like to calculate the mean ADP of a structure model (PDB) from a Python script using tools in CCTBX/PHENIX. I tried to find out how and dig it from Python source code but I have been unsuccessful yet. Please, how to do it (in Python)? Although It is quite easy to calculate it in on my own directly from PDB for isotropic ADPs, the situation can be a bit complicated for anisotropic ADPs... Thank you. Best regards, Martin Mal ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 04 Jun '21

04 Jun '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JUN 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Twinned data with Phaser
by Thomas, Leonard M. 25 May '21

25 May '21

Hello, I have been working on a structure for a very long while. We have a number of data sets with the good ones mostly around the 3.1-3.2 A range. I do have a determination of the structure but would like to see if I can get the structure determined with a slightly higher resolution data set at around 2.7 A. Problem is the 2.7 data is twinned. Are there settings in Phaser to handle twinned data or is the twinning only handled during refinement? Thank you for any advice, outside of forgetting about the twinned data. 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

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Problems with sharpening in Autosharpen
by Carlos HENRIQUE FERNANDES 25 May '21

25 May '21

Dear all, I am facing some problems with sharpening in Autosharpen. My current map is about 3.2 Å resolution, which I obtained after CTF-Refinement and Polishing in Relion. When I use Autosharpen in default parameters, it tells me that are applied an overall Bsharp applied of 220.34 and a final Biso of 87.42; but very little sharpening is done; I was unable to observe a typical helices sharpening at this value of resolution. I did some tests setting progressive Bsharp values (240; 260; 280; 300), but I am still unable to visualize a typical helices sharpening. Has anyone had problems like that? Any tips? Thanks in advance, Carlos.

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Exclude atoms from real space refinement
by Florian Nachon 23 May '21

23 May '21

Hello, I want to exclude a residue from XYZ refinement, but I noticed that my atom selection "not (chain A and resid 100)" is ok for reciprocal-space, but not real-space? Someone encounter a similar problem 10 years ago: http://www.phenix-online.org/pipermail/phenixbb/2012-December/019297.html Is it a known bug? Any clues? Thanx in advance — Florian

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Fwd: [SRCC #47733] Fwd: Phenix GUI showing unreadable squares
by Dong-Hua Chen 19 May '21

19 May '21

Hi All, I asked Stanford cluster admin and he is questioning the CentOS version incompatibilities (see the following). Any suggestions? Thanks Dong-Hua ---------- Forwarded message --------- From: Kilian Cavalotti <srcc-support(a)stanford.edu> Date: Thu, May 13, 2021 at 12:20 PM Subject: Re: [SRCC #47733] Fwd: [phenixbb] Phenix GUI showing unreadable squares To: <donghua.chen(a)gmail.com> Hi Dong-Hua, It looks like the software is built for CentOS 6.10, while Sherlock is running CentOS 7.x, so incompatibilities are likely. Is there a way to rebuild it from source. maybe? Cheers, -- *Kilian Cavalotti* Stanford Research Computing Center *Sherlock // *web <https://www.sherlock.stanford.edu> | docs <https://www.sherlock.stanford.edu/docs> | status <https://status.sherlock.stanford.edu> | news <https://news.sherlock.stanford.edu>47733:1231609

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Cryo-EM Facility Manager - Berkeley California
by Paul Adams 18 May '21

18 May '21

Dear Colleagues, I would like to draw your attention to a job opening here in Berkeley California, for a Cryo-EM Facility Manager: https://lbl.referrals.selectminds.com/jobs/cryo-em-facility-manager-3801 This position requires expertise in biological cryo electron microscopy (cryo-EM). The successful candidate will be responsible for maintaining the in-house transmission electron microscopes (TEMs) and accessory equipment in excellent working order as well as training new users, scheduling access, and assisting with the collection of high-quality data. Duties will include providing complex technical support for sophisticated biotech-laboratory equipment including maintenance, calibration, repair and troubleshooting of instrumentation, control systems, experimental apparatuses, computers, and peripheral equipment as well as coordinating and scheduling vendor related maintenance and repairs. This is a full time, 3 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion. Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Deadline today -- IUCr SARS-CoV-2 special symposia.
by Pearce, N.M. (Nick) 17 May '21

17 May '21

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural biology of coronaviruses This session covers new structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. - New methods to fight the pandemic This session covers new methods in crystallography and structural biology to better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in computational methods, beamline instrumentation and integrative structural biology. - Crystallography against Corona This session covers the efforts of the crystallographic community to find drug candidates for COVID-19 both in-silico and in the lab by using structural models of viral proteins. - Using crystallography for education during the pandemic Using crystallography for education during the pandemic *** Please submit your abstracts today! If this isn’t possible, email us to let us know you intend to submit an abstract in the coming days! *** For each session, 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Session co-chairs

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questions about using experimental phases in phenix.refine
by David A Case 15 May '21

15 May '21

I'm trying to use experimental phases derived from an cryoEM density map do carry out reciprocal space refinement in phenix.refine. I used phenix.map_box to get the map coefficients, and then the CCP4 program chltofom (with the -colin-phifom flag) to create the HL coefficients from F/PHI computed from the electron density map. 1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set: | normalized target function (mlhl) (work): -5862.311069 | | target function (mlhl) not normalized (work): -6438670043.811632 and attempted refinements more or less destroy my protein and increases both the mlhl target value and the R-factors. Is there an example data set I could access to help me find out what I'm doing wrong? (Using the ml target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to work well, and has a postive target function, but seems sub-optimal if phase information is available.) 2. Is there a way to do a "simple" least-squares refinement, minimizing sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as vectors? Does the ls target perhaps do this if use_experimental_phases=True? Usual apologies if there is some great tutorial on this that I've not found. ...thanks...dave case

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Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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Scientific software programmer at UCLA
by Johan Hattne 12 May '21

12 May '21

Dear all; The Gonen lab at UCLA's Department of Biological Chemistry is looking for a research specialist in scientific software programming to develop software for computational biological image analysis. The Gonen lab works toward understanding how membrane proteins help cells maintain homeostasis. To that end, the lab studies channels, transporters, and receptors, structurally and functionally. More information about the lab can be found by visiting https://cryoem.ucla.edu/. Details about the position and application instructions here: https://hhmi.wd1.myworkdayjobs.com/External/job/University-of-California-Lo… // Best wishes; Johan

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Help with den refine
by Alex Singer 12 May '21

12 May '21

Hi: I recently installed the Linux-64 version of phenix1.19.2-4158 and used the command line to run phenix.den_refine. The command was just Phenix.den_refine xxx_refine_25.pdb xxx_refine_25.mtz (xxx is just the name of the project, and is made up, but I did the same thing for two different projects) And then it ran for a while until it started the initial minimization before the den routine, ie coordinate minimization before annealing and then it crashed with the error message TypeError: %d format; a number is required, not Autotype I believe this is a python error, but is there something straight-forward that I can do about this so that den_refine can work? Thanks for your help Dr. Alex U. Singer

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