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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 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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