- phenixbb - phenix-online.org

Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 06 Mar '24

06 Mar '24

Dear Colleagues, The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> October 13 - 29, 2024 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Covered Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) 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) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

1 0

map display after resolve_cryoem
by Valerie Biou 01 Mar '24

01 Mar '24

Hello, I ran resolve_cryoem for solvent flattening and obtained a ccp4 map that behaves like a mask both in Coot and Chimera. the histogram is just a single line and the dimensions are different from my original map, even though in a second run I used restore_full_size = true in a second run. To be clear, my original map has 480^3 dimensions, and the output one is 125x140x224, which boxes my protein but I can't see the inside of the map. I guess there is something I didn't understand. Can you please help me? All the best, Valerie Valérie Biou, Ph.D. valerie.biou(a)ibpc.fr Laboratoire de Biologie Physico-Chimique des Protéines Membranaires umr7099.ibpc.fr <http://umr7099.ibpc.fr/> UMR 7099 CNRS/Univ. Paris-Cité Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099

1 0

Re: [phenixbb] Joint X-ray / neutron refinement
by Kristoffer Lundgren 24 Feb '24

24 Feb '24

Hello phenixbb, When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at https://phenix-online.org/documentation/reference/refinement.html#neutron-a… as a template I get some error messages (running phenix.refine from the command line): Unrecognized PHIL parameters: ----------------------------- xray.refinement.refine.strategy (file "joint_xn.eff", line 33) xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37) xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48) neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49) neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50) Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine. Best regards Kristoffer From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / neutron refinement Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

3 2

Ordered solvent in phenix.refine
by Oliver H. Weiergräber 23 Feb '24

23 Feb '24

Hello, after switching from version 1.20 to 1.21, I noticed that the updated list of waters generated by the ordered_solvent option in phenix.refine is no longer numbered sequentially; it seems a final re-numbering step is now skipped. Is this intentional? Of course it can be advantageous to keep waters from changing their numbers, e.g. if they are part of occupancy groups. On a related note, is there a mechanism to protect certain "important" waters from being deleted while all the rest is updated as usual? One obvious option would be a dedicated chain ID, but afaik phenix.refine accepts a chain ID for output but not for input waters ... Best regards, Oliver ================================================== Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ==================================================

2 1

Rotamer error in real space refinement
by Nikos Pinotsis 23 Feb '24

23 Feb '24

Hi, I am using real space refine with the latest phenix 1.21-5207 for fitting a model into a cryoEM map. During refiment one Trp goes clearly out of density (vertical to the density) although the map is very well defined at this part of the protein. I tried local_grid_search either for every cycle or last, however it didn't fix the problem. I know that this is reported a couple of years ago as fixed (dev-4218), I am wondering if something changed during the last version. Another solution I can think it to keep the side chain of this Trp fixed. How can I do that? thanks Nikos -- ________________________________________ Nikos Pinotsis Associate Professor Biochemistry, Department of Chemistry National and Kapodistrian University of Athens

2 1

Define bond between O3' of a nucleotide to P of 3DR HETATM ligand (abasic nucleotide)
by Mark Saper 23 Feb '24

23 Feb '24

I need to create a phosphodiester bond between O3’ of a DNA nucleotide and P of a 3DR HETATM ligand (a modified nucleotide). I also need to delete O3P of the 3DR nucleotide. How can I create this restraint? Also, how can I get COOT to display this bond? Thanks, Mark _____________________ Mark A. Saper, Ph.D. Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

2 1

Tenure track position in Protein Science for Pathogen Defense
by Cygler, Miroslaw 20 Feb '24

20 Feb '24

Dear Colleagues, I am excited to let you know that the Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, is searching for an exceptional candidate in the area of Protein Science for Pathogen Defense, to fill a tenure-track Canada Research Chair (CRC) Tier 2 position. The CRC program is the flagship of a national strategy to make Canada one of the world's top countries in research and development. We are looking for an outstanding early career scientist to establish and lead a groundbreaking research program in protein science to understand the mechanisms of bacterial and viral infection in humans or animals, to investigate host-pathogen interactions, or to discover novel mechanisms of defense against known and potential future pathogens. Within this broad scope, specific areas of interest include synthetic antigen design, the molecular basis of immune response to pathogens, mechanisms of antimicrobial resistance, and the prediction-guided design of artificial antibodies. We are interested in hiring a world-class expert in one or more of the following areas: (i) protein structure prediction and structural bioinformatics, (ii) protein design, and (iii) cryo-electron microscopy. A detailed advertisement with instruction how to apply is enclosed and can also be viewed here: <https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> Canada Research Chair (CRC) Tier 2 in Protein Science for Pathogen Defense<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> protection.outlook.com<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> [X]<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> . Regards, Mirek ======================================================= Dr. Miroslaw Cygler, FCAHS Professor, Dept. Biochem, Microbiol & Immune, U. of Saskatchewan Canada Research Chair in Molecular Medicine Using Synchrotron Light Health Sciences Building 3D30.6 (Box 9) 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada Email: miroslaw.cygler(a)usask.ca<mailto:[email protected]> Website: http://research-groups.usask.ca/cyglerlab/ Phone: 306-966-4361, cell: 306-203-2317 =======================================================

1 0

Structural Biology Workshop, June 10-12, 2024, Arlington, VA
by Meilleur, Flora 15 Feb '24

15 Feb '24

Dear All, We would like to bring to your attention the 2024 Neutrons in Structural Biology workshop. This workshop will highlight the need for next-generation instruments and toolsets for structural biology, with a focus on neutrons and other complementary techniques, and the development of integrated experimental and computational frameworks that connect them. Neutrons in Structural Biology - Challenges & Opportunities June 10-12th 2024 Sheraton Pentagon City Hotel, Arlington, VA. For details and registration see: Neutrons in Structural Biology - Challenges & Opportunities<https://conference.sns.gov/event/402/> The workshop will include a 1-day satellite training workshop (June 10, 2024) to educate graduate students and postdoctoral researchers in the application of neutron techniques in structural biology. A limited numbers of travel awards are available to support graduate students and post-doctoral fellows attendance at the workshop. The travel award application deadline is April 12, 2024. Details here<https://conference.sns.gov/event/402/page/2891-travel-awards-deadline-april…>. Flora Meilleur on behalf of the organizing committee: Andrey Kovalevsky Flora Meilleur Dean Myles Hugh O'Neill Flora Meilleur, Ph.D. Neutron Scattering Scientist Neutron Sciences Directorate Oak Ridge National Laboratory Professor Molecular & Structural Biochemistry N C State University Editor, Journal of Applied Crystallography Office: 865-576-2779

1 0

to leave atoms out of ADP restraints
by Jorge Iulek 13 Feb '24

13 Feb '24

Hi, all, The ADP restraints I refer to in this discussion are the ones that would make B-factors of nearby atoms to influence (or more or less resemble) each other. For some very disordered side chains, I would like to test "taking out" the "more disordered" atoms (maybe for high chi angle variability) of these restraints, for them to be more free to skyrocket, but also that they do not influence so much the main chain, in some cases where the flexibility difference between main and side chain seems to be significant. Is there a way to do so? Thanks, Jorge

2 2

helical structure - Real space refinement
by Dmitry Semchonok 01 Feb '24

01 Feb '24

Dear colleagues, Is there any specific procedure for Real space refinement in Phenix, having a map and model when working with helical structure? Many thanks Kind regard, Dmitry

2 1