- phenixbb - phenix-online.org

Improvement of low resolution MR phases
by Kajander, Tommi A 29 Jun '21

29 Jun '21

Hello all, I was wondering what would be current best protocols for trying to improve maps/phases for low resolution MR / refinement solutions (5-6 Å resolution). High solvent content of course, dimeric 2:2 protein complex so some NCS averaging and density modification I assume might help (related structures known, currently maps very blobby, clear solution but I think should be able to do better...). Also, refinement suggestions welcome. Best route in phenix? So far worked initially with ccp4. Other suggestions also welcome. Thanks! Tommi Tommi Kajander, Ph.D. Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki, Finland p. +358-50-4480991 http://www.helsinki.fi/kajanderlab

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Macromolecular Crystallography - CSHL Course
by Paul Adams 24 Jun '21

24 Jun '21

Dear Colleagues, The July 16th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 4 through October 19, 2021 is rapidly approaching. Please see the attached announcement, and the official course web site is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=21 please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. We anticipate holding the course in person as long as the pandemic situation continues to improve. Appropriate COVID-19 precautions will be followed to ensure the safety of all participants. Everyone will be required to provide documentary proof of a prior FDA or EMA approved vaccine. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2021 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO), Tom Peat (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be data collection at state-of-the-art beamlines at NSLS-II. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This course is supported with funds provided by the National Institute of General Medical Sciences for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tom, Tassos, Paul, and Jim > Begin forwarded message: > > From: Cold Spring Harbor Laboratory Meetings & Courses <meetmail(a)cshl.edu> > Subject: Macromolecular Crystallography - CSHL Course > Date: June 24, 2021 at 5:20:20 AM PDT > To: pdadams(a)lbl.gov > Reply-To: meetmail(a)cshl.edu > > > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > October 4 - 19, 2021 > Application & Materials Deadline: July 16 > We anticipate that the vaccine situation may sufficiently improve to allow us to offer this course safely in-person. > > All participants will be required to provide documentary proof of a prior FDA or EMA approved vaccine. > Instructors > Janet Newman, CSIRO, Australia (likely remote) > James Pflugrath, Rigaku Americas Corporation (ret.), Texas > Anastassis Perrakis, Netherlands Cancer Institute > Paul Adams, Lawrence Berkeley National Laboratory > Co-Instructor: > Tom Peat, CSIRO, Australia(likely remote) > X-ray crystallography has been the cornerstone of structural biology for half a century, and remains the technique of choice for atomic resolution understanding of macromolecules and for structure guided drug discovery. This intense course combines laboratory and computational instruction to train course participants in the major techniques used to determine three-dimensional structures. It is designed for scientists with a working knowledge of protein structure and function, but who are new to macromolecular crystallography or who wish to increase their in-depth knowledge of macromolecular crystallography. > Topics to be covered include > Basic diffraction theory > Crystallization (proteins, nucleic acids, complexes and membrane proteins) > Synchrotron X-ray sources and optics > Data collection and processing > Structure solution by experimental phasing methods (SAD, MAD, MIR, and others) and molecular replacement > Electron density maps improvement > Model building and refinement > Structure validation > Coordinate deposition > Structure presentation > If you are interested in applying for this course please let us know by submitting the Expression of Interest form via the course website as soon as possible. > Please click this link to go to the Macromolecular Crystallography course website for further info. <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > > > Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 > -- 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 <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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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 14 Jun '21

14 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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