- phenixbb - phenix-online.org

ALS Webinar April 10th
by Paul Adams 05 Apr '23

05 Apr '23

Dear Colleagues, A reminder that we will be hosting a webinar (registration link below) that provides information for the synchrotron structural biology user community about accessing the resources at the Advanced Light Source in Berkeley. This is timely because of the imminent closure of the Advanced Photon Source for a year for their upgrade. Synchrotron capacity for biosciences research will be significantly impacted, and we want to be sure that the community has information about alternative facilities during the APS dark time. http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10t… The webinar will cover capabilities at the beamlines in macromolecular crystallography, small angle X-ray scattering, and X-ray footprinting, as well as information on how to apply for beamtime. While the webinar is of most relevance to the US research community, we welcome participation by anyone who is interested. Cheers, Paul -- 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 33, Room 250 Building 978, Room 4126 Building 977, Room 268 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: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

1 0

Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 03 Apr '23

03 Apr '23

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark. online posting: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2023, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar-transporting and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Bavnhøj et al. “Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10” Nature Plants 7 (2021) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 15. May. 2023. See deails here: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s…

1 0

restraints_edits.params -- inquiries -- issues
by p.auffinger 30 Mar '23

30 Mar '23

Hi phenix users, I started to add restraints to a large ribosomal file by using the file (in full) below. I encountered two issues: 1) The first one is: how to use this file in the GUI? It seems to get rejected while its accepted when I run phenix through the command line. 2) The second is: restraints involving water molecules with residue numbers > 9999 get rejected. Could that limit be overcome through a future patch? ### refinement.geometry_restraints.edits { MG_8078 = chain 0 and resname MG and resid 8078 and name MG W_12641 = chain 0 and resname HOH and resid 12641 and name O bond { action = *add atom_selection_1 = $MG_8078 atom_selection_2 = $W_12641 symmetry_operation = None distance_ideal = 2.2 sigma = 0.1 slack = None } } ### Thanks for any thoughts on this, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr -----

2 1

27th Annual SCSB Structural Biology Symposium - Registration NOW OPEN
by White, Mark 21 Mar '23

21 Mar '23

You and your colleagues are cordially invited to join us for the 27th Annual Structural Biology Symposium to be held on April 29, 2023 in Levin Hall, UTMB Galveston. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: Yunfeng Chen Ph.D. Univ. of Texas Medical Branch Ruben L. Gonzalez Jr., Ph.D. Columbia University John A. Tainer, Ph.D. University of Texas MD Anderson Cancer Center David W. Taylor, Ph.D. University of Texas Junjie Zhang Ph.D. Texas A&M University To register or for more information, visit https://scsb.utmb.edu/symposium Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, UTMB, Galveston, TX 409.747.4747 https://xray.utmb.edu ________________________________

1 0

Save the date! “Not the GRC” on Diffraction Methods in Structural Biology 2024
by Winter, Graeme (DLSLtd,RAL,LSCI) 17 Mar '23

17 Mar '23

Good afternoon all, “Not the Gordon Research Conference” on Diffraction Methods in Structural Biology 2024 - Experiments and Measurements Organisers: Graeme Winter, Kunio Hirata (NTGRC-chairs) Helena Taberman, Ali Ebrahim (NTGRS-chairs) Local organisers - Arwen Pearson, Ashwin Chari As you will have seen from a message from James Holton last year, the GRC have decided that the 2024 meeting on Diffraction Methods will not be further supported. We are not deterred! A number of the GRC ex-chairs and those nominated for chairing the next meeting feel that this opportunity for the diffraction methods community to come together is important enough that it should continue to happen, even without GRC support. We are therefore delighted to launch the “Not-the-GRC Diffraction methods in Structural Biology”. The topic of the meeting will be “Experiments and Measurements” and we have a great lineup of speakers in mind. Where: https://www.harnackhaus-berlin.mpg.de/en When: 21st - 27th July 2024 i.e. about when the next diffraction methods meeting would have been. Starting with the model of the GRC, since we collectively believe it is a fantastic meeting, we plan to make a few improvements (better accommodation and acoustics, fewer minimum attendees to keep the feel of a small meeting) and we will keep the equivalent of the GRS before the main meeting, as well as the free afternoons for collaborative discussion, and the strong emphasis on being able to talk to everyone. We will also keep the focus on new ideas and so follow the protocol of not recording presentations and encouraging the presentation of unpublished data and ideas. With that in mind, this will be a small meeting (100-120 maximum) so there will be an application process and we will open registration in January 2024. We also want as many early career people as possible - the last GRC was refreshing and fun with a lot of new faces, and this is something we want to build on. So, please hold the date in your calendar and we look forward to sharing the scientific programme with you in the coming months and seeing many of you in Berlin next summer. All the best Graeme, Kunio, Helena, Ali, Arwen and Ashwin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

1 0

Postdoc positions in cryo-EM development at the MRC Laboratory of Molecular Biology, Cambridge UK
by Jan Löwe 13 Mar '23

13 Mar '23

*Postdoctoral positions available in cryo-EM methods development at the MRC Laboratory of Molecular Biology, Cambridge UK, in the groups of Chris Russo and Jan Löwe* We have one position each available, funded for two years as part of the LMB’s Blue Sky collaboration with AstraZeneca. The project, in collaboration with Kasim Sader at AZ aims to develop novel methods to overcome problems with sample denaturation and preferred orientation during vitrification of thin aqueous films. Ideas involve outrunning the processes involved and modifying the air-water interfaces. The ultimate goal is to make cryo-EM sample preparation a much more universal (and enjoyable) process. Cryo-EM experience will be beneficial and a strong desire to engage deeply in technical developments is a must. The LMB and AZ provide everything required, including a highly collaborative and friendly environment, as well as one of the world’s best institutional cryo-EM setups, including state-of-the-art machine and electronics workshops, a clean room dedicated to grid fabrication, and soon four Titan Krios microscopes. More details and on how to apply are here: https://www.nature.com/naturecareers/job/12796284/postdoctoral-scientist-st… https://www.nature.com/naturecareers/job/12796280/postdoctoral-scientist-st… Chris, Kasim and Jan Jan Löwe MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK Email: jyl(a)mrc-lmb.cam.ac.uk Phone +44 1223 26 7644 Website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl Christopher J Russo  MRC Laboratory of Molecular Biology  Cambridge, CB2 0QH, UK Email: crusso(a)mrc-lmb.cam.ac.uk  Phone +44 1223 26 7535 Website http://www.mrc-lmb.cam.ac.uk/crusso/

1 0

Local restraints
by Luca Pellegrini 07 Mar '23

07 Mar '23

How can I freeze a set of atoms in phenix.real_space_refine? I've got an arginine side chain that is consistently misplaced during refinement, and I’d like to restrain its movement. I notice that refinement.geometry_restraints.edits.scale_restraints is not available anymore, is there another way? Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 3

Two postdoctoral positions at CNB-CSIC, Spain
by Carmen San Martin 23 Feb '23

23 Feb '23

Dear all, Please find here information on two open positions on structural biology / protein design: https://saco.csic.es/index.php/s/gFm9EKLMNBWD2G8 Regards, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 (internal: 432228) Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://wwwuser.cnb.csic.es/~sanmartinlab http://www.microscopia.org ------------------------------------------------------------

1 0

Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023
by Armando Albert 19 Feb '23

19 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

1 0

(no subject)
by Armando Albert 06 Feb '23

06 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

1 0

Solving MR solution without sequence information
by Rosenberg, Eric (NIH/NCI) [F] 06 Feb '23

06 Feb '23

Hi all, I'm in a bit of bind here and am seeking some advice. For context, a former graduate student in our lab set crystal trays of an MBP fusion protein, the fused part after MBP being ~400 amino acids long. This region is also predicted to be mostly unstructured, but has a C-terminal SH3 domain. Our graduate student then graduated and before throwing out some of her trays a year or two later, we found some hits of the MBP fusion protein that actually diffracted to 2.9 Angstrom. I spent some time working on it after we collected the data (June 2021), but because I didn't know what crystallized specifically, it was impossible to phase, and replicating seemed next to impossible, too. The Matthew's coefficient was predicting ~130 amino acids in the ASU, space group C222 or C2221. Since whatever crystallized was clearly a degradation product of the MBP fusion, I tried phasing with SH3 domains and a lot of other things to no avail. As a final last ditch effort I eventually submitted the .mtz file to SBGrid to perform a Wide Search MR job, and low and behold it actually found MR solutions that had TFZ scores ~17 in space group C2221! So here's my current situation-I have been able to phase the data set using the MR search model, but again, I don't know what specifically it is that I've crystallized. I'm currently able to get the Rfree to ~0.4, but can't seem to improve it. I am really at a loss of what to do, since there are obvious backbone issues with the protein (as seen from iterative build composite omit maps), but every time I try to manually correct them it seems to make the Rfree worse. The MR solution does not align very well at all to the MBP fusion, only ~20 identity, and again, I don't know to which ~130 amino acids I crystallized out of the ~400 of the MBP fusion. Is it one continuous stretch, two copies of a shorter stretch, etc.? I tried phasing with a polyalanine model of the MR search model and then tried autobuilding just a polyalanine sequence to get the backbone right, but that doesn't seem to work. Autobuild also fails when trying to various fragments of the MBP fusion sequence. Other than opening coot and manually building the entire polypeptide chain, is there an easier method? I think that once the backbone is totally right the phases will improve so I can start putting in side chains, but I'm not sure. My latest effort is to just use Sculptor prior to Phaser in order to force the sequences to match, but again, I don't know precisely what sequence was crystallized. I have tried both the Phenix and CCP4 software suites, for reference. Any and all help would be much appreciated (and yield an acknowledgement on a paper, if this ever works). Best, Eric Rosenberg CRTA Postdoctoral Fellow Randazzo Lab Laboratory of Cellular and Molecular Biology National Cancer Institute, US

4 4

Re: [phenixbb] Solving MR solution without sequence information
by Dom Bellini 04 Feb '23

04 Feb '23

1 0

Re: [phenixbb] Solving MR solution without sequence information
by Kay Diederichs 03 Feb '23

03 Feb '23

Hi Eric, I'd try the following: 1) use SIMBAD to potentially find other/better models 2) use ISOLDE for model building - maybe ask Tristan Croll for help 3) submit your best model to the DALI server to retrieve closer models HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

1 0

Postdoctoral position in YSBL, University of York
by Jon Agirre 31 Jan '23

31 Jan '23

Dear all, Applications are invited for a Postdoctoral Research Associate position, funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in the Department of Chemistry. The successful applicant will join a vibrant team of researchers at the heart of the world-leading York Structural Biology Laboratory (YSBL). The work of the laboratory over the years has included the delivery of world-leading methods and experimental discoveries, training and nurturing hundreds of outstanding scientists in the process. Role In collaboration with Dr. Elisa Fadda (Maynooth University, Ireland), we have developed proof-of-concept software that models protein glycosylation into AlphaFold models. This task has been automated and integrated into the new Python interface of the carbohydrate-specific Privateer software. In parallel, we have developed infrastructure and analyses that allow us to get a clear picture of glycans and their interactions. We expect that this technology will enable the successful applicant to, based on existing glycobiological knowledge, extend the Privateer software to predict, build and adapt models of glycans onto AlphaFold models. Main duties and responsibilities: - To develop and extend the Privateer software to predict, build and adapt models of glycans onto AlphaFold models. - To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the Protein Data Bank and the AlphaFold Protein Structure Database. For informal enquiries: please contact Dr Jon Agirre, jon.agirre(a)york.ac.uk To apply: https://jobs.york.ac.uk/vacancy/research-associate-513495.html Department The Department of Chemistry is one of the largest and most successful departments at York and we are renowned internationally for our research. As a department, we strive to provide a working environment that allows all staff and students to contribute fully, to flourish, and to excel. We are proud of our Athena Swan Gold Award. The Department of Chemistry values all employees for the qualities and skills they bring to the workplace and aims to be a diverse and egalitarian community in which all can thrive. Many thanks for making it this far in the advert! With best wishes, Jon -- Dr Jon Agirre [image: A button with "Hear my name" text for name playback in email signature] <https://www.name-coach.com/jon-agirre> Royal Society Olga Kennard Research Fellow CCP4 ED&I champion | instruct-ERIC representative @ 3D-Bioinfo (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @glycojones

1 0

Feb 9 Free Webinar: New Dimensions - How Computation Is Accelerating Structure Based Drug Design
by Mitchell D. Miller 31 Jan '23

31 Jan '23

Dear all, On Thursday, February 9, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Karen Akinsanya, President of Research & Development - Therapeutics, Schrödinger, Inc will present a zoom webinar titled New Dimensions - How Computation Is Accelerating Structure Based Drug Design This zoom webinar is free, but registration is required. Please see the registration link on the National Academies of Sciences, Engineering, and Medicine event page along with Karen Akinsanya's abstract and bio. https://www.nationalacademies.org/event/02-09-2023/new-dimensions-how-compu… A flyer for the webinar is also available https://www.nationalacademies.org/documents/embed/link/LF2255DA3DD1C41C0A42… This is the second presentation in the series -- Advancing Drug Discovery: A Webinar Series of the National Academies of Sciences, Engineering, and Medicine The series is being hosted jointly by the U.S. National Committee for Crystallography (USNC/Cr), the U.S. National Committee for the International Union of Pure and Applied Chemistry (USNC/IUPAC) and the U.S. National Committee for CODATA. More information about the series is on the NASEM website and it will be updated as additional webinars in the series are confirmed. The website also has links to recordings of "past events". https://www.nationalacademies.org/our-work/advancing-drug-discovery-a-webin… Please forward this to any you think would be interested. Sincerely, Mitch P.S. for those who missed the January 10, 2023 webinar presented by Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation on Pandemic Preparedness: Accelerating the Discovery of New Therapeutics The recording is available on the National Academies of Sciences, Engineering, and Medicine event page along with Ken Duncan's abstract and bio. https://www.nationalacademies.org/event/01-10-2023/pandemic-preparedness-ac…

1 0

RapiData at SSRL 2022 - application deadline extended by two weeks!
by Smith, Clyde 12 Jan '23

12 Jan '23

We have extended the deadline for applications for a place at the RapiData 2022 @ SSRL workshop to next Friday, February 4th 2022! There are still a few spots left, so get your application in! The workshop will be held virtually from May 4 - 14 2022. The course will comprise lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). There will also be several days of software tutorials (HKL3000,XDS, CCP4/DIALS, Phenix, AutoSharp/AutoProc, Shelx, Coot) and you will all get to connect remotely to the SSRL beamlines to collect both monochromatic and MAD/SAD data. There is also an opportunity to ship your own samples to SSRL prior to the workshop, and collect your own data. Please visit https://www-ssrl.slac.stanford.edu/rapidata/rapidata-2022/index.html and use the links on the "registration" page to apply for the course. Successful applicants will be notified later in February 2022 and invited to register at that time (there will be no fee for registration). Regards, Clyde Smith (csmith(a)slac.stanford.edu) and Silvia Russi (srussi(a)slac.stanford.edu) Workshop Organizers

1 3

Jan 10 Free Webinar: Pandemic Preparedness: Accelerating the Discovery of New Therapeutics
by Mitchell D. Miller 03 Jan '23

03 Jan '23

Dear all, On Tuesday, January 10, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation will present a zoom webinar titled Pandemic Preparedness: Accelerating the Discovery of New Therapeutics This zoom webinar is free, but registration is required. Please see the registration link on the National Academies of Sciences, Engineering, and Medicine event page along with Ken Duncan's abstract and bio. https://www.nationalacademies.org/event/01-10-2023/pandemic-preparedness-ac… A flyer for the webinar is also available https://www.nationalacademies.org/documents/embed/link/LF2255DA3DD1C41C0A42… This is the first presentation in a new series -- Advancing Drug Discovery: A Webinar Series of the National Academies of Sciences, Engineering, and Medicine The series is being hosted jointly by the U.S. National Committee for Crystallography (USNC/Cr), the U.S. National Committee for the International Union of Pure and Applied Chemistry (USNC/IUPAC) and the U.S. National Committee for CODATA. More information about the series is on the NASEM website and it will be updated as additional webinars in the series are confirmed. https://www.nationalacademies.org/our-work/advancing-drug-discovery-a-webin… Please forward this to any you think would be interested. Sincerely, Mitch

1 0

staraniso/phenix.refine
by Andrea Piserchio 22 Dec '22

22 Dec '22

Dear all, I am trying to validate and then (hopefully) deposit a structure generated using the autoproc/staraniso staraniso_alldata-unique.mtz file as input for phenix.refine. Autoproc also produces a cif file ( Data_1_autoPROC_STARANISO_all.cif) specifically for deposition. Long story short, the PDB validation server complains about the lack of a freeR set for both files. I realized that, at least for the cif file, the r_free_flag is missing (but why does the .mtz for the isotropic dataset work??),so I then tried to use for validation the *.reflections.cif file that can be generated by phenix.refine. This file can actually produce a validation report, but I still have some questions: 1) Is it proper to use the .reflections.cif file for this purpose? During the upload I do see some errors (see pics); also, the final results show various RSRZ outliers in regions of the structure that look reasonably good by looking at the maps on coot, which seems odd ... 2) In case the *.reflections.cif is not adequate/sufficient for deposition (I sent an inquiry to the PDB, but they did not respond yet), can I just add a _refln.status column to the autoproc cif file (within the loop containing the r_free_flag) where I insert “f” for r_free_flag = 0 and “o” everywhere else? Thank you in advance, Andrea

5 7

Labeling centric and acentric reflections
by Andre LB Ambrosio 22 Dec '22

22 Dec '22

Hi, Is there a way to label centric and acentric reflections in the .mtz file and output an additional column, let's say, with values 0 (acentric) and 1 (centric), similar to R_free flags? Many thanks for your attention. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba

2 4

Re: [phenixbb] staraniso/phenix.refine
by Gerard Bricogne 21 Dec '22

21 Dec '22

Dear Andrea, As Clemens Vonrhein is not not subscribed to the phenixbb, I am sending the message below on his behalf. With best wishes, Gerard. ---------------------------------------------------------------------------- Dear Andrea, Besides the paragraph in the Release Notes of our latest BUSTER release that Luca directed you to, you may find it useful to consult the following Wiki page: https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif Although it has not yet been updated so as to mention explicitly the cases where refinement was done with REFMAC or phenix-refine, the procedure and commands given there will work in these two cases as well. Our intention was to get feedback from our users first, then to announce the extended capability of aB_deposition_combine more broadly - but your question clearly shows that we should make that announcement sooner rather than later. Getting back to your message: although uploading either the phenix-generated mtz file or the mmCIF file generated by aB_deposition_combine would be acceptable to the OneDep system, we would highly recommend using those from aB_deposition_combine for several reasons. First of all, these files should already contain the data from Phenix but also provide additional data blocks with richer reflection data (and metadata!), going right back to the scaled and unmerged data without any cut-off applied. Furthermore, it should ensure that the correct data quality metrics (i.e. merging statistics) are included into the mmCIF files uploaded during deposition. Of course, you don't need to use aB_deposition_combine to generate such a set of mmCIF files (model and reflection data) - these are after all just text files - but the devil is often in the details. It may be useful to add some fairly general background information in order to avoid misunderstandings and false impressions - so here are some relevant points you may wish to consider. (a) The deposition of model and associated data into the PDB should allow for two things: (1) the validation of the current model and of its parametrisation on their own, as well as a check against the data used during refinement, and (2) the provision of additional data to allow further analysis of, and improvements to, the data handling as well as the model itself. For the first task one needs to deposit the data exactly as used by the depositor to arrive at the current model, i.e. the input reflection data (as used as input to the refinement program) plus all available Fourier coefficients (as output by that refinement program) needed to compute the maps used in modeling. The second task requires deposition of less and less "processed" versions of the experimental data - ultimately going back to the raw diffraction images. This might involve several sets of reflection data, e.g. (i) scaled, merged and corrected reflection data, (ii) scaled and merged data before correction and/or cutoff, and (iii) data scaled and unmerged before outlier rejection - plus additional variants. (b) When going from the raw diffraction images towards the final model, a lot of selection and modification of the initial integrated intensities takes place - from profile fitting, partiality scaling, polarization correction, outlier rejection, empirical corrections or analytical scale determination and error model adjustments, all the way the application of truncation thresholds (isotropically, elliptically or anisotropically), conversion to amplitudes (and special treatment of weak intensities) and anisotropy correction. There are often good reasons for doing all or some of these (with sound scientific reasons underpinning them - not just waving some "magic stick"), even if under special circumstances a deviation from standard protocols is advisable. What is important from a developer's viewpoint is to provide users with choices to influence these various steps and to ensure that as many intermediate versions of reflection data as possible are available for downstream processes and deposition. (c) At deposition time, the use of a single reflection datablock is often not adequate to provide all that information (e.g. refinement programs might output not the original Fobs going in, but those anisotropically rescaled against the current model - so a second block might be needed to hold the original Fobs data, free from that rescaling). If different types of map coefficients are to be provided, they too need to come in different mmCIF datablocks (2mFo-DFc and mFo-DFc for observed data only; 2mFo-DFc filled in with DFc in a sphere going out to the highest diffraction limit; 2mFo-DFc filled in with DFc for only the reflections deemed "observable" by STARANISO; F(early)-F(late) map coefficients for radiation damage analysis; coefficients for anomalous Fourier maps etc). So ultimately we need to combine (going backwards): the refinement output data, the refinement input data and all intermediate versions of reflection data (see above) ... ideally right back to the scaled+unmerged intensities with a full description of context (image numbers, detector positions etc). This is what the "Data Processing Subgroup" of the PDBx/mmCIF Working Group has been looking at extensively over the last months, and about which a paper has just been submitted. (d) autoPROC (running e.g. XDS, AIMLESS and STARANISO) and the STARANISO server provide multi-datablock mmCIF files to simplify the submission of a rich set of reflection data. autoPROC provides two versions here: one with traditional isotropic analysis, and the another for the anisotropic analysis done in STARANISO. It is up to the user to decide which one to use for which downstream steps. To help in combining the reflection data from data processing with that from refinement, and in transferring all relevant meta data (data quality metrics) into the model mmCIF file, we provide a tool called aB_deposition_combine: it should hopefully work for autoPROC (with or without STARANISO) data in conjunction with either BUSTER, REFMAC or Phenix refinement results. At the end the user is provided with two mmCIF files for deposition: (1) a model file with adequate data quality metrics, and (2) a reflection mmCIF file with multiple datablocks all the way back to the scaled+unmerged reflection data. (e) It is important at the time of deposition to not just select whatever reflection data file happens to be the first to make it through the OneDep system, as this can often lead to picking up the simplest version of an MTZ or mmCIF file, but to choose, if at all possible, the most complete reflection data file containing the richest metadata. Otherwise we simply increase the number of those rather unsatisfying PDB entries whose reflection data files contain only the very minimum of information about what they actually represent and what data quality metrics (such as multiplicity, internal consistency criteria etc) would have been attached to them in a richer deposition. *** Please note that the current OneDep system seems to complain about the fact that unmerged data blocks come without a test-set flag column: this looks to us like an oversight, since test-set flags are attributes belonging to the refinement process, so that it makes no logical sense to require them for unmerged data. This will probably requires some rethinking/clarification/changes on the OneDep side. A final remark: Instead of trying to give the impression that there is only one right way of doing things, and therefore only a single set of reflection data that should (or needs to) be deposited, it would seem more helpful and constructive to try and provide a clear description of the various "views" of the same raw diffraction data that can be provided by the various approaches and data analysis methods we have at our disposal. Together with more developments regarding the PDBx/mmCIF dictionary, and coordinated developments in the OneDep deposition infrastructure, this will enable better and richer depositions to be made, helping future (re)users as well as software developers. Cheers, Clemens ---------------------------------------------------------------------------- -- On Mon, Dec 19, 2022 at 05:42:24PM -0500, Andrea Piserchio wrote: > So, > > Both the phenix-generated mtz file (silly me for not checking this first) > and the cif file generated by aB_deposition_combine can be uploaded on the > PDB server. > > Thank you all for your help!! > > Andrea > > On Sat, Dec 17, 2022 at 5:06 PM Pavel Afonine <pafonine(a)lbl.gov> wrote: > > > Hi, > > > > two hopefully relevant points: > > > > - phenix.refine always produces an MTZ file that contains the copy of > > all inputs plus all is needed to run refinement (free-r flags, for > > example). So if you use that file for deposition you have all you need. > > > > - Unless there are strongly advocated reasons to do otherwise in your > > particular case, you better use in refinement and deposit the original > > data and NOT the one touched by any of available these days magic sticks > > (that "correct" for anisotropy, sharpen or else!). > > > > Other comments: > > > > > - However, CCP41/Refmac5 does not (yet) read .cif reflection files. As > > > far as I know, Phenix Refine does not (yet) neither. > > > > Phenix supports complete input / outputs of mmcif/cif format. For > > example, phenix.refine can read/write model and reflection data in cif > > format. It's been this way for a long time now. > > > > Pavel > > > > > > On 12/16/22 17:32, Andrea Piserchio wrote: > > > Dear all, > > > > > > > > > I am trying to validate and then (hopefully) deposit a structure > > > generated using the autoproc/staraniso staraniso_alldata-unique.mtz > > > file as input for phenix.refine. > > > > > > Autoproc also produces a cif file ( Data_1_autoPROC_STARANISO_all.cif) > > > specifically for deposition. > > > > > > Long story short, the PDB validation server complains about the lack > > > of a freeR set for both files. I realized that, at least for the cif > > > file, the r_free_flag is missing (but why does the .mtz for the > > > isotropic dataset work??),so I then tried to use for validation the > > > *.reflections.cif file that can be generated by phenix.refine. This > > > file can actually produce a validation report, but I still have some > > > questions: > > > > > > 1) Is it proper to use the .reflections.cif file for this purpose? > > > During the upload I do see some errors (see pics); also, the final > > > results show various RSRZ outliers in regions of the structure that > > > look reasonably good by looking at the maps on coot, which seems odd ... > > > > > > 2) In case the *.reflections.cif is not adequate/sufficient for > > > deposition (I sent an inquiry to the PDB, but they did not respond > > > yet), can I just add a _refln.status column to the autoproc cif file > > > (within the loop containing the r_free_flag) where I insert “f” for > > > r_free_flag = 0 and “o” everywhere else? > > > > > > > > > Thank you in advance, > > > > > > > > > Andrea > > > > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://phenix-online.org/mailman/listinfo/phenixbb > > > Unsubscribe: phenixbb-leave(a)phenix-online.org > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 0

Re: [phenixbb] centered triclinic lattice
by Cathy Lawson 15 Dec '22

15 Dec '22

Many thanks to all those who followed up with me both on and off the list. I notice now that 1LKS structure factors include hkl indices that violate reflection rules for A1 (general: k + l = 2n). The reflections in violation would have to be removed in order to reindex to the well-known primitive triclinic for lysozyme. Knowing this, reindexing is not a viable option, so the update will need to be P1 with ncs (either via explicit coordinates or matrix set).

1 0

anomalous signal to ~5.1 - 4.5Å
by Damon Wei 15 Dec '22

15 Dec '22

Dear colleagues, During the past few days, I have been trying to perform Experimental Phasing (SAD) using AutoSol. I am really curious to know if any of you have ever had any successful experience for phasing with anomalous signal only to ~5.1 - 4.5Å. In this scenario, will you use the default value (2.38 Å) in the “high-resolution limit” option in AutoSol, or a higher value like ~ 3-4 Å? How will you set the options including NCS copies, thoroughness, and resolution for running HySS? Any replies and help will be greatly appreciated! Best, Damon

2 3

centered triclinic lattice
by Cathy Lawson 14 Dec '22

14 Dec '22

Looking for suggestions — cctbx/phenix seems not to be able to handle a triclinic lattice with centering. Specific Example: PDB entry 1LKS with cell parameters/space group “A 1”: CRYST1 31.970 65.080 27.250 94.57 111.56 82.98 A 1 2 A 1 diagram: http://img.chem.ucl.ac.uk/sgp/large/001bz1.htm <http://img.chem.ucl.ac.uk/sgp/large/001bz1.htm> Are there any other options for working with this data in phenix other than creating an explicit 2nd copy of the coordinates at x, 1/2+y,1/2+z and setting space group to primitive lattice P 1? Thanks in advance.

4 5

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 05 Dec '22

05 Dec '22

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JAN 2023. 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. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

1 0

Reminder - 3rd CCP4/BGU workshop on Data Collection and Structure Determination
by Anat Shahar 05 Dec '22

05 Dec '22

Dear All, We would like to remind you that the registration deadline for the 3rd CCP4/BGU workshop on Data Collection and Structure Determination is on 20th December. You are all welcome to hurry up and ensure your place. The 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including “how to apply”, registration form and tentative program, can be found at: https://lifewp.bgu.ac.il/wp/ccp4workshop/ Best wishes, Anat Shahar & Eugene Krissinel [cid:[email protected]] Anat Shahar, PhD Macromolecular Crystallography Research Center (MCRC) Ilse Katz Institute for Nanoscale Science & Technology Ben-Gurion University of the Negev Beer-Sheva, Israel Tel: +972-8-6461807 Web: www.bgu.ac.il/crystallography<http://www.bgu.ac.il/crystallography>

1 0