- phenixbb - phenix-online.org

Senior Technician Position at the Biochemistry and Structural Biology Unit - IEO Milano
by Sebastiano Pasqualato 11 Jan '21

11 Jan '21

Dear all, a position is open at the Biochemistry and Structural Biology Unit of the European Institute of Oncology in Milan. The Unit (https://www.research.ieo.it/research-and-technology/technological-units/bio… <https://www.research.ieo.it/research-and-technology/technological-units/bio…>) is one of the technological platforms of the Department of Experimental Oncology of the European Institute of Oncology (www.research.ieo.it <http://www.ieo0researh.it/>), a comprehensive cancer centre located in the south area of Milan. We provide services and support to the department in the fields of Biochemistry and Structural Biology and collaborate both with scientific groups of the department and external ones to foster the structural biology aspects of their projects. The ideal candidate has a Master/PhD degree in Chemistry, Biotechnology or Biology, with strong interest in biochemistry and structural biology. We are looking for an enthusiastic, motivated person, with good organisational and relational skills, and a good knowledge of English. She/he will take care of assisting scientists collaborating with the Unit in macromolecular samples purification, characterisation and crystallisation, managing sample shipment to synchrotrons, supervising instrumentation usage and maintenance. The Unit is setting up a Cryo-EM lab with an in-house VitroBot blotting device and external Electron Microscopy access, which the candidate is expected to manage. Experience in setting up grids and Cryo-EM data collection will be a distinguishing skill. Potential applicants are encouraged to contact Dr. Sebastiano Pasqualato, sending a brief description of interests, and a CV with at least one referee contact to sebastiano.pasqualato(a)ieo.it <mailto:[email protected]>. Best regards, Sebastiano -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web: https://www.research.ieo.it/research-and-technology/technological-units/bio…

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Postdoc position available on membrane proteins at Aarhus University
by Joseph Lyons 11 Jan '21

11 Jan '21

Dear Colleagues, Please pass this along to anyone who might be interested. Thanks! Joe online posting: http://tiny.cc/y1y7tz We are looking for a highly skilled and motivated postdoc with an interest in working on structural studies of lipid transporting membrane transporters by cryo-EM. The applicant should preferably have a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from Spring 2021, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total maximum of 3 years. The position: The position aims to strengthen ongoing activities in the newly established Lyons Lab at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on lipid transport systems. The lab houses facilities for mammalian protein production, purification, cellular, biochemical and biophysical characterization and data processing and has access to the state-of-the-art Cryo-EM facility based at iNANO (https://inano.au.dk/research/research-platforms/inano-cryo-em-facility/). The group is part of the Section of Structural Biology at Aarhus University. The project is within the framework of a highly prestigious and international collaborative research program ASAP (Aligning Science Across Parkinson’s), the team will explore the structure, function and regulation of the human glucosylceramide transporters (ATP10) (https://parkinsonsroadmap.org/research-network/biology-of-pd-associated-gen…). These molecular insights may pave the way for a drug discovery strategy for Parkinson’s disease. 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 and/or functional characterization 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 - a full-time appointment (100%) as a post doc for a period of 3 years with the possibility of an extension. The successful candidate is encouraged to initiate and participate in grant proposals to expand the research line and ensure continuation after the project end - Participation in a vibrant international research network ASAP with focus on collaboration and open science, offering excellent networking opportunities. - access to a well-developed research infrastructure. - 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. Deadline: All applications must be made online (http://tiny.cc/y1y7tz) and received by 7th Feb. 2021.

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About Restrain Files for ligands
by Sharan Karade 08 Jan '21

08 Jan '21

Hello all, I hope everybody is doing well. Happy New Year 2021!!! I am stuck with some unusual behavior of restrain files generated by Phenix.ReadySet. I crystallized the protein with ligands which have double bonds between the atoms. As I see clear electron density for the ligand, I drew a ligand molecule in Coot (Ligand builder) and fitted in electron density very nicely. Until here, I can see the double bonds in the modelled ligand. I generated the restrain files using Phenix.ReadySet to further proceed for refinement. Unfortunately, after refinement the double bonds were converted to single bonds. I tried to generate new restrain files and refined the model, resulting in similar output. But, fortunately in one case, the double bonds were retained after refinement also. I tried to repeat with other ligands, where I was unsuccessful to retain the double bonds. please help me. Thank you so much. Regards Sharan -- Sharan Karade Postdoc-fellow IBBR-UMD, 9600 Gudelsky Dr, Rockville Maryland 20850

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Modeling sugars with Coot and Phenix
by Emilia C. Arturo (Emily) 07 Jan '21

07 Jan '21

Hello All, I have several questions regarding sugar modeling. These are questions for both Coot (0.9.4-pre/CCPEM) and Phenix (1.18.2-3874) usage (on a Mac) for modeling as correctly as possible several N-linked glycosylation (i.e. not ligand) sugars within a protein, and about the approach as it pertains to higher resolution X-ray maps (better than 2A) or to lower resolution EM maps (~3-4A). I am new to the world of glycoproteins and cryoEM, not new to model building or X-ray crystallography, and would welcome any advice or insight. For relatively low resolution maps, where sugar moieties cannot be placed unambiguously, in theory (say Agirre (2017) and Emsley and Crispin (2018)) pyranose placement within the map should be quite highly restrained by ideal geometry for the specific sugar expected from prior knowledge. In practice, however, it’s not entirely clear how to maintain these restraints on pyranose geometry and conformation during manual building in Coot, or how to apply any special restraints in Phenix. The Glyco module of Coot does indeed place fine looking Asn-NAGs after a few iterations of manual placing and refining to account for the poor resolution of the acetyl group, just as discussed by Emsley and Crispin (2018). However, the validation report that is obtained from the OneDep system at the rcsb web server for the resulting structure shows many outliers in bonds and angles within the NAG or between the NAG and protein Asn residue. In Coot I have experimented with various restraints (in the R/RC menu), including decreasing the Refinement weight/weight matrix to zero, or some small non-zero number, thinking this places less weight on the map signal and more on the ideal values within Coot’s libraries. I have tried a variety of refinement restraint combinations in Coot to address individual bonds and angles outliers within the sugar, but the rcsb validation report still finds departures from ideal geometry. Meanwhile, in Phenix I don’t do anything specific for the refinement of glycosylation sugars (should I?) other than apply the appropriate restraints for any low resolution EM map; are there specific restraints files I ought to be using within Phenix real space refine jobs for N-linked sugars? Then I noticed that loads of existing PDB entries containing N-linked glycans contain similar outliers in pyranose geometry. So this prompted me to wonder whether we’re not doing things right, that in practice we’re not correctly following what’s advised in theory, or whether this is just the state of model building currently. Could someone more experienced than am I on sugar building please comment here on how exactly to get the sugars better built? e.g. what buttons to press and why, in Phenix and/or in Coot. Or is this a tolerable situation where sugar geometries differ from ideal even at low resolution? Is it perhaps a matter of different targets being used for PDB validation by the rcsb versus by Coot? It turns out that regarding higher resolution maps I am also unsure of exactly how to apply restraints within Coot. For example, using PDB ID 5VAA and its map with a reported resolution of 1.55A, I centered on Asn297 and its associated glycosylation sugars. I experimented with refinement strategies (i.e. the settings of R/RC), thinking that the best approach would be little restraint on ideal geometry and higher weight on the map signal. But no matter what combination of restraints I used, I was unable to keep the model locally from distorting; i.e. the deposited model versus map looks great, but within Coot I find a hundred ways to destroy it. I must be doing something wrong. Any advice or references you’d recommend would be greatly appreciated. Thanks. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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post-doc position at KU Leuven, ligand-gated ion channels
by Chris Ulens 05 Jan '21

05 Jan '21

A post-doctoral position is available at the Laboratory of Prof. Chris Ulens, KU Leuven, Belgium (http://www.xtal.be <http://www.xtal.be/>). The research in the Laboratory of Structural Neurobiology is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our methods rely on X-ray crystallography and cryo-EM in combination with electrophysiological recordings and fluorescence-based techniques. Our laboratory hosts an integrated macromolecular crystallization facility with a Mosquito crystallization robot and two RockImagers. We have access to a 200 kV Glacios microscope on campus as well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current projects are situated at the crossroads of structural elucidation and drug discovery of different pentameric ligand-gated ion channels. We would like to recruit a post-doc with prior experience in cryo-EM or X-ray crystallography of membrane proteins. The successful candidate: - easily communicates in an open verbal manner and has a team player spirit - has an ambitious work ethic - critically contributes to writing of manuscripts and grant proposals - makes efforts to obtain independent funding - meets intermediate deadlines and brings projects to a successful end - fuels internal discussions of recent publications in the field - sets an example to younger PhD students in the lab - identifies directions for future scientific research The position is open immediately and applications will be accepted until the position is filled. Applicants are requested to submit a CV with publication list and two references. E-mail to chris.ulens(a)kuleuven.be <mailto:[email protected]> Selection of recent publications: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4. Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511. The structural basis for an on-off switch controlling Gβγ-mediated inhibition of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117.

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Bad geometry for DNA after Real-Space-Refine
by Jobichen Chacko 05 Jan '21

05 Jan '21

Dear BB, I am using phenix real space refinement for refining a cryo-EM model of protein-DNA complex. However after refinement the structure of the dna strands are twisted in a very bad geometry compared to the initial input model. I am using version 1.8 for this project, also tried couple of other versions as well, but the same problem happened. How to rectify this issue? Thank you. Jobi

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Variation in bonds after loading restraints
by Vatsal Purohit 01 Jan '21

01 Jan '21

Hello, I’ve been having issues with obtaining consistent number of bonds after generating .cif files using eLBOW. To generate the .cif file for an NADH molecule on eLBOW, I’ve been using a SMILE string generated using Chemdraw and a template .pdb file that was generated after using LigFit with a ligand .pdb model (also initially generated using a SMILE string). However, I find that when I load the restraints the bonds in the molecule only show correctly on the older version of coot (0.8.9.2). The double bonds on the adenine ring don’t appear in the latest version of coot (0.9.3) and the double bonds on the molecule don’t show up at all when I load the .cif file on REEL. Is there a reason why they could be inconsistent? Could I be viewing them incorrectly on REEL? Any thoughts on this would be appreciated! I’ve attached the SMILE string, template .pdb file and final .cif file in this email for your reference. Regards, Vatsal PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University PULSe-Biophysics and Structural Biology training group vpurohi(a)purdue.edu<mailto:[email protected]> | 346-719-9409

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Calculating the transformation matrix of density map alignment
by Ahmad Khalifa 23 Dec '20

23 Dec '20

I have two density maps that I'm trying to align, or more precisely, calculate the transformation matrix (rotation and translation) of their alignment (moving one map and aligning it with the other map). Is there a way to accomplish that using phenix or any other tool? Thanks a lot and happy holidays.

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Post-doctoral vacancy in cryoEM of viruses
by Hasan, Syed Saif 22 Dec '20

22 Dec '20

Dear Colleagues, A vacancy for a post-doctoral researcher is available immediately in my lab in the University of Maryland Center for Biomolecular Therapeutics located on the campus of Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses utilize structural similarities with host proteins to hijack inter-organelle communication. Prior experience in insect cell culture for recombinant protein production is desirable. Expertise in cryoEM or X-ray crystallography will be advantageous. Candidates who have recently completed their PhD are encouraged to apply. IBBR is located 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 kV Talos Arctica with a Falcon 3EC DED and a 200 kV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have a Vitrobot Mark IV and a Cp3 cryo-plunger for sample preparation. We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. Interested candidates should send their CV and a cover letter to me at sshasan(a)som.umaryland.edu ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Coot+Phenix issue
by Ashima Chopra 21 Dec '20

21 Dec '20

Hi all, I am running a refinement on Phenix for one structure, as I work on the Molprobity corrections from another refined structure in Coot. My Coot connects to Phenix so I can navigate through the Molprobity list easily, however the tmp.refine files from the first refinement keep popping up and replacing the current maps I have open. Is it possible to be connected to Phenix and define which project to display the maps/models from? Thanks, Ashima Ashima Chopra Graduate Assistant Eddy Arnold Laboratory Department of Chemistry and Chemical Biology/ Center for Advanced Biotechnology and Medicine Rutgers University, New Brunswick

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ASAPpdb - pledge to release data with preprints
by James Fraser 16 Dec '20

16 Dec '20

Fellow structural biologists - The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable. There is nothing more disappointing than reading a great preprint and not being able to open the coordinates and inspect the density! Sign the pledge to publicly release PDB files (and associated structure factor, restraint, and map files) with deposition of preprints here: https://asapbio.org/asappdb All the best, James PS> Apologies for the cross post to multiple bb's -- James Fraser - http://www.fraserlab.com - @fraser_lab jaimefraser(a)gmail.com // jfraser(a)fraserlab.com he/his/him (please do NOT use james.fraser(a)ucsf.edu)

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MicroED workshop 2020
by Johan Hattne 13 Dec '20

13 Dec '20

Dear all; We are pleased to announce the 6th MicroED workshop to be held on December 21, 2020. This will be a free virtual event. Please register at the following website to receive your link https://cryoem.ucla.edu/course Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover 1. Sample preparation methodologies 2. EPU-D for data collection 3. Camera systems and performance 4. FIB-milling procedures for soluble and membrane protein samples 5. Data analysis software, refinement, and structure solution The schedule is available on the registration page. // Sincerely; The organizing committee (Tamir Gonen, Brandon Mercado, Brent Nannenga)

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Submission Deadline on December 14th
by Tessa Van Grack 07 Dec '20

07 Dec '20

Hi PHENIX community, The AIMS Awards Fall 2020 application deadline is just one week away! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development programs, and get published. We encourage investigators, postdocs, and graduate students worldwide to apply. The AIMS Awards program provides non-profit researchers with virtual screening and compounds for physical testing at no cost. Collaborate with us to find novel active compounds for your protein target of interest. You can fill out the short application form directly on the website: atomwise.com/aims <https://hubs.la/H0z3sT80>. Please don't hesitate to reach out to me if you have any questions! Kind regards, Tessa *Tessa Van Grack, M.S.* Partnering Associate Atomwise <https://www.atomwise.com/> | Better Medicines Faster ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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Re: [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
by Folmer Fredslund 03 Dec '20

03 Dec '20

Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct. I hope this helps Folmer tor. 3. dec. 2020 05.48 skrev Igor Petrik <petrik1(a)illinois.edu>: > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >

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Re: [phenixbb] 2x Postdoc positions and Lab Manager position
by Gordon Joyce 03 Dec '20

03 Dec '20

The Joyce Laboratory, Henry M. Jackson Foundation supporting the Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research have openings for two postdoctoral positions and a Lab Manager position in Structural Biology of Emerging Infectious Diseases. One postdoctoral position involves the structural and biochemical characterization of small molecule inhibitors against Emerging Infectious pathogens including SARS-CoV-2, as part of an integrated drug development pipeline at WRAIR. One postdoctoral position involves the structural and biochemical characterization of viral glycoproteins from Emerging Infectious pathogens including SARS-CoV-2 to enable vaccine development, antibody therapeutics and small molecule inhibitors. The Lab manager position will oversee day-to-day activities in the lab including lab inventory, ordering and routine mammalian cell culture and transient transfection. These positions offer a unique opportunity to gain extensive structural biology experience focused on vaccine and therapeutic development for pandemic prevention. Interested candidates should apply at the sites indicated below, or with a cover letter and a current CV directly to Gordon Joyce gjoyce(a)eidresearch.org<mailto:[email protected]> Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Lab Manager: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… M. Gordon Joyce, Ph.D. Chief, Structural Biology The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) In support of the Emerging Infectious Diseases Branch (EIDB) and the US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 https://eidresearch.org/our-team/m-gordon-joyce-phd gjoyce(a)eidresearch.org<mailto:[email protected]> ********************************************************************** This message contains information that may be confidential, privileged, proprietary, or otherwise protected. If you are not the intended recipient, notify the sender immediately and delete/destroy all copies of this message and any attachments. This message is not intended to constitute or include either an electronic record or an electronic signature unless otherwise specifically indicated.

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Power disruption (12/1 11 pm to 12/2 2 pm)
by Billy Poon 02 Dec '20

02 Dec '20

Hi everyone, Sorry for the short notice, but due to some electrical work in our building, several of the Berkeley servers will be shut down later tonight at 11 pm Pacific and will return tomorrow afternoon at 2 pm Pacific. This will affect: - The Phenix web site (http://phenix-online.org/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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alpha-Fold 2?
by lbetts0508 01 Dec '20

01 Dec '20

all - I just read the blurb in Nature Briefing about the DeepMind AI having made a big advance in the CASP protein fold prediction. Does it sound really transformational, does it work for membrane proteins - all the usual questions come to mind. Do we know enough yet about it? Signed an old protein crystallographer, L. Betts

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map_to_model input labels
by Schnicker, Nicholas J 20 Nov '20

20 Nov '20

Hi All, I'm trying to run map_to_model via command line for the first time (clearly) with an mtz file from an X-ray dataset. I have tried different iterations, but I can't seem to come up with the correct syntax for suppling the input labels. It gives me the list of available labels below, but what is the correct syntax to provide for input? Available labels: ['IMEAN,SIGIMEAN', 'I(+),SIGI(+),I(-),SIGI(-)', 'F,SIGF,DANO,SIGDANO,ISYM', 'F(+),SIGF(+),F(-),SIGF(-)', 'FreeR_flag'] Sorry I have checked the documentation, but still managed to fail. Thanks for your help, Nick

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Ensemble refinement with covalent ligands - bond length > 5Å
by Schulz, Eike-Christian 18 Nov '20

18 Nov '20

Dear all, I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking. However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length? Best, Eike ———————————————————————————— Dr. Eike C. Schulz Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 | 22761 Hamburg | Germany Building 99 (CFEL) | Office O2.101 Phone +49 (0)40 8998-6264<tel:%2B49%20%280%2940%208998-6264> | Fax +49 (0)40 8994-6264<tel:%2B49%20%280%2940%208994-6264> | Website www.mpsd.mpg.de<http://www.mpsd.mpg.de/>

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phenix.refine last cycle often break geometry for no obvious improvement
by Clement Degut 18 Nov '20

18 Nov '20

Hi, I regularly encounter this problem with phenix.refine, happened to me with several structures, at wildly different resolution, so as described in the title, phenix.refine seems to break perfect geometry in its last cycle (put 3 5 or 10 it's the last), for no obvious improvement in term of other metrics, actually getting the temporary file just before the last cycle had given me very good result in the past. Is there a reason for this behaviour? A way to get back PDB at a certain point of the refinements cycles would be really great actually. example of what I refer to: [image: image.png] Cheers, Clément Dégut PDRA Dr M Plevin's group University Of York

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Diamond-II MX beamlines letters of support
by David Briggs 18 Nov '20

18 Nov '20

Dear all, (Apologies for the slightly off-topic cross-post - hopefully, this will be of interest to all MX practitioners, not just Diamond light source users.) As Diamond User Committee MX representatives, we'd just like to remind you that the deadline for letters of support for Diamond-II beamline upgrades is this Friday, 20th November. As you are perhaps aware, the Diamond machine is scheduled for a major upgrade to a 4th generation source 2025-2027. Further information about the upgrade can be found here<https://www.diamond.ac.uk/Home/About/Vision/Diamond-II.html>. All MX beamlines will benefit from a brighter, more focused source – however, two MX beamlines have been selected as flagship projects for significant upgrades. I04-1 > K04 Ultra XChem. The I04-1 fixed wavelength beamline used for the XChem fragment screening will be completely rebuilt as K04. Briefly, K04 will allow higher throughput fragment screening (meaning more projects and more fragments can be screened) and it is hoped the improved characteristics of the Diamond-II beam will allow XChem methodologies to be extended to more difficult targets such as transmembrane proteins. The K04 proposal outline can be found here<https://www.diamond.ac.uk/dam/jcr:bd879384-900b-4a2c-897d-a8e0e818c6e8/MX%2…> [PDF]. I24 > KMX Kinetic micro crystallography. The I24 microfocus beamline will be upgraded to enhance the capabilities of I24 and allowing analysis of smaller crystals, radiation-sensitive crystals, and expanding the serial synchrotron crystallography (SSX) functionality of the beamline. The abilities to conduct room temperature SSX will also be enhanced to allow in-crystal kinetic analysis, with various on-line spectroscopic (Raman, UV-Vis, XES) detectors built into the end station. The KMX proposal outline can be found here<https://www.diamond.ac.uk/dam/jcr:add3277b-5bc2-4e8b-93a2-25d1e0e585f6/MX%2…> [PDF] Having read these proposals you will obviously be very excited by the possibilities and will want to submit your letters of support for both of them, by Friday, 20th November Letters of support can be submitted via this link<https://forms.office.com/Pages/ResponsePage.aspx?id=dLonnQABDU2B_x1yja6N9sO…>. Thanks in advance, Dave & Arnaud. -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == Diamond User Committee MX representative == about.me/david_briggs 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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Postdoctoral position in cryo-EM and translation regulation
by Loveland, Anna 13 Nov '20

13 Nov '20

Postdoctoral position in cryo-EM and translation regulation ‒ from bacteria to neurons Korostelev Lab, University of Massachusetts Medical School We study how the ribosome interacts with numerous cellular components to achieve high accuracy and efficiency of gene expression. We’d like to understand the key roles of translation and ribosomes in: (1) Neurodevelopment and neurodegenerative diseases; (2) Bacterial stress signaling and gene regulation (e.g. coupling with transcription); and other aspects of gene expression (https://www.umassmed.edu/korostelev-lab/). We use a range of approaches, including cryo-EM and biochemistry (see selected references below). Our laboratory is housed at the RNA Therapeutics Institute, a vibrant and highly interactive research community: https://www.umassmed.edu/rti/about-the-rti/faculty-members/. Our colleagues are interested in nearly all aspects of RNA biology, from small to large RNAs to RNA chemistry and therapeutics development. We seek a highly motivated person who very recently received a PhD, or will soon receive a PhD. Applications sent prior to the dissertation defense date are welcome. If you are interested in using single-particle cryo-EM and in situ (cellular) EM to elucidate cellular mechanisms, submit the following information to ann.powers(a)umassmed.edu<mailto:[email protected]>: 1) Your CV (including your publication list); 2) Cover letter (less than 2 pages) describing: (i) your previous work - focusing on your most interesting finding(s), (ii) your scientific interests, (iii) which aspects of translation regulation are of interest to you. 3) Email addresses of three references. Selected publications (accessible via the provided links): • Carbone CE, Demo G, Madireddy R, Svidritskiy E, Korostelev AA. “ArfB can displace mRNA to rescue stalled ribosomes<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.natur…>”. Nature Commun. 2020. • Loveland AB, Demo G, Korostelev AA. “Cryo-EM of elongating ribosome with EF-Tu GTP elucidates tRNA proofreading<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.natur…>”. Nature. 2020. • Loveland AB, Svidritskiy E, Susorov D, Lee S, Park A, Demo G, Gao FB, Korostelev AA. “Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM<file:///C:/Users/PowersA/Dropbox%20(UMass%20Medical%20School)/Korostelev/Job%20Postings/Susorov%20D%20et%20al.%20%22Termi-Luc:%20a%20versatile%20assay%20to%20monitor%20full-protein%20release%20from%20ribosomes>”. bioRxiv. 2020. • Susorov D, Egri S, Korostelev AA. "Termi-Luc: a versatile assay to monitor full-protein release from ribosomes<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frnajourna…>”. RNA. 2020. • Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. “Extensive ribosome and RF2 rearrangements during translation termination<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2019. • Loveland AB, Demo G, Grigorieff N, Korostelev AA. “Ensemble cryo-EM elucidates the mechanism of translation fidelity<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fem.rdcu.be…>”. Nature. 2017. • Demo G, Rasouly A, Vasilyev N, Svetlov V, Loveland AB, Diaz-Avalos R, Grigorieff N, Nudler E, Korostelev AA. “Structure of RNA polymerase bound to ribosomal 30S subunit<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2017. • Abeyrathne PD, Koh CS, Grant T, Grigorieff N, Korostelev AA. “Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.…>”. eLife. 2016. • Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA. “Ribosome•RelA structures reveal the mechanism of stringent response activation<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2016. https://twitter.com/korostelevlab<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.c…> --- Anna Loveland, Ph.D. anna.loveland(a)umassmed.edu 617 610 4321 (cell) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

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A chance to develop new therapies through AI molecular screening
by Tessa Van Grack 12 Nov '20

12 Nov '20

Hi PhenixBB community, We are excited to announce the opening of the AIMS Awards Fall 2020 cycle! Collaborate with us to find novel active compounds for your protein target of interest. Our AIMS Awards program provides non-profit researchers with virtual screening and compounds for physical testing at no cost. For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development programs, and get published. The program is open to investigators, postdocs, and graduate students worldwide. You can apply directly on the website: atomwise.com/aims <https://hubs.la/H0z3sT80>. Please don't hesitate to reach out to me if you have any questions! Kind regards, Tessa *Tessa Van Grack, M.S.* Partnering Associate Atomwise <https://www.atomwise.com/> | Better Medicines Faster ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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phenixbb Digest, Vol 180, Issue 1 : Using a CryoEM density for MR
by Claudia Millán Nebot 10 Nov '20

10 Nov '20

Dear Almudena, I'm assuming that you were testing the full mr phaser section in phenix and tried the add map ensemble. This expects an mtz containing structure factors, and where certain preparation has been done. A full description of the steps required can be found in a prior publication ( https://www.nature.com/articles/nprot.2015.069?proof=t) from our group. In short, you'll need to first convert your mrc map to structure factors (there a command line utility for this in phenix, called map_to_structure_factors). But you can't input this directly as an ensemble, a series of other steps involving placing the map in a large P1 cell using phenix.cut_out_density (wit the option for_phaser set to True) will also be required for it to work, and you'll need to give information about the center and the extent of your map, as well as an estimation of the errors in the map (in form of an rmsd). Only then you'll be able to use the density for MR. Within the framework of the new version of phaser under development, phasertng, we are working on facilitating this MR approach, making it automatic and robust, and investigating about the best ways to treat the maps and to parameterise their search. This is work in progress but we have already some modes for map preparation for MR within phasertng, so we will also be happy, if you share with us the file off-line, to provide you with the prepared structure factors file. Otherwise, if you need any help in following the steps of the previous protocol, we will also provide the support. Best wishes, Claudia El jue., 5 nov. 2020 a las 12:41, <phenixbb-request(a)phenix-online.org> escribió: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: Number of unique reflections (John Berrisford) > 2. Fwd: Re: Number of unique reflections (Boaz Shaanan) > 3. Computational Crystallography Newsletter (CCN) submissions > (Nigel Moriarty) > 4. Phenix User Workshop, 17th and 18th of November (Paul Adams) > 5. Anomalous signal (Shramana Chatterjee) > 6. Re: Anomalous signal (Roger Rowlett) > 7. Re: Anomalous signal (Gerg? G?gl) > 8. mrc maps as a molecular replacement model > (Almudena Ponce Salvatierra) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 20 Oct 2020 18:30:16 +0100 > From: "John Berrisford" <jmb(a)ebi.ac.uk> > To: "'Pavel Afonine'" <pafonine(a)lbl.gov>, "'Armando Albert'" > <xalbert(a)iqfr.csic.es>, <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Number of unique reflections > Message-ID: <009401d6a706$ad6c8120$08458360$(a)ebi.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear Armando and Pavel > > During the deposition process we compare two values > > _reflns.number_obs > > http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_ > obs.html > <http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number…> > And > _refine.ls_number_reflns_obs > > http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb > er_reflns_obs.html > <http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_num…> > > We expect the number of observed reflections to be higher (or the same) as > the number of reflections used in refinement. > We would expect that these two mmCIF items handle Friedel pairs > consistently > - if the number of reflections observed is reported with Friedel pairs > separately then the number of reflections in refinement should also report > Friedel pairs separately. > > My assumption here is that there is a mismatch in reporting these values. > > Hope this helps > > John > > -----Original Message----- > From: phenixbb-bounces(a)phenix-online.org > <phenixbb-bounces(a)phenix-online.org> On Behalf Of Pavel Afonine > Sent: 20 October 2020 18:16 > To: Armando Albert <xalbert(a)iqfr.csic.es>; phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Number of unique reflections > > Hi Armando, > > > We have realise that the output mtz and mmcif files duplicate the > > number of miller indices (the number of unique reflections) with > > respect to those in the mtz input file. We guessed that this > > correspond to the friedel pairs, > > data handling machinery in Phenix (cctbx) counts F+ and F- as separately, > that is (1, 1, 2) and (-1, -1, -2) are two entries, not one. > > > but it is annoying for pdb submission, as the server warns that the > observations measured are less that those used in the refinement. > > What shall we do fro correct this issue? > > Perhaps talk to PDB stuff and suggest to make the process less annoying... > > I'm not sure what we can do at our end. I guess if we count them as one > then > I'm sure some one will come around asking 'why you are counting two > reflections as one?'. > > Pavel > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > ------------------------------ > > Message: 2 > Date: Tue, 20 Oct 2020 18:16:16 +0000 > From: Boaz Shaanan <bshaanan(a)bgu.ac.il> > To: phenixbb <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Fwd: Re: Number of unique reflections > Message-ID: <787a9a55-8840-44ad-b176-a7d3feae038c(a)email.android.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: < > http://phenix-online.org/pipermail/phenixbb/attachments/20201020/739082e7/a… > > > > ------------------------------ > > Message: 3 > Date: Mon, 2 Nov 2020 14:38:52 -0800 > From: Nigel Moriarty <nwmoriarty(a)lbl.gov> > To: undisclosed-recipients:; > Subject: [phenixbb] Computational Crystallography Newsletter (CCN) > submissions > Message-ID: > <CANkP= > 2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Folks > > The deadline for submissions to the Computational Crystallography > Newsletter (CCN) is 15 DEC 2020. Please consider writing an article of > general interest to the community. > > The Computational Crystallography Newsletter (CCN) is an electronic > newsletter for structural biologists, and is published online every 6 > months. Feature articles, meeting announcements and reports can be > submitted to me at any time for consideration. Submission of text by > email or word-processing files using the CCN templates is requested. > Past newsletters and a Microsoft Word template are available at > www.phenix-online.org/newsletter. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov >

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Table 1 Issue 2
by Xavier Brazzolotto 10 Nov '20

10 Nov '20

I've downloaded the 1.19rc5-4047 version of Phenix and the Table 1 issue is still present. Table 1 does not output macromolecule, ligand and water specific values for « Number of non-hydrogen atoms » and « Average B-factor » items. Still on OSX Xavier

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