- phenixbb - phenix-online.org

phenix.refine command lane xyz restrains
by Błażej Bagiński 24 Aug '22

24 Aug '22

Dear Phenix community, lately I started toying with the terminal version of our favourite refinement software (on kubuntu linux). I'm refining a structure with a ligand that is not in the refmac database (.cif file needed), and I couldn't find anything on how to implement xyz coordinates restraints for the procedure. In other words, I have a ligand that I built into the polder map and I want to tell the software "do not change the positions in space of these atoms". How can I do that? Also, side question: why there are three different(?) versions of command line phenix.refine for every phenix installation? What is the difference between them? REMARK 6 I followed the online guide for "Refinement at high resolution" on my 1,2~1,3A structure and the results were surprisingly nice, I'd say potentially even better than usually used parameters in GUI (5 cycles both). Kind regards, Blazej

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Postdoctoral Research Associate in the Structural Biology of Supramolecular Protein Assemblies
by Owen Davies 19 Aug '22

19 Aug '22

Dear all, I would like to advertise a postdoctoral position that is currently available in my lab at the Wellcome Centre for Cell Biology, University of Edinburgh, UK (https://www.wcb.ed.ac.uk/research/owen-davies). This position is for an initial period of three years (with possibility to extend), to work on the integrative structural biology of the synaptonemal complex. The synaptonemal complex is a supramolecular protein structure that assembles during meiosis to facilitate homologous chromosome synapsis and crossover formation. Its immense structure, of many micrometers in length, is formed through the combination of at least three unique self-assembling protein systems, which individually form lattice-like arrays, para-crystalline filaments and 'intermediate filament'-like fibres. This position aims to determine the molecular structure of the human synaptonemal complex and its constituent complexes through their reconstitution from recombinant proteins. This will be achieved through a cutting-edge structural biology approach, involving cryo-EM single particle reconstruction and tomography, structure solution of components by X-ray crystallography, solution biophysics (including X-ray and light scattering, and single-molecule biophysics), and the integration of experimental findings by advanced computational modelling of structures and assembly dynamics. The post is funded by a Wellcome Senior Research Fellowship, and will be hosted in a well-equipped and well-funded lab, which includes the following: Extensive biochemical equipment (including numerous Akta Pure systems, SEC-MALS etc) Protein production and characterisation facility (https://www.ed.ac.uk/biology/research/facilities/edinburgh-protein-producti…) State-of-the-art biophysics equipment (including C-trap optical tweezers) In-house TEM, SEM and newly upgraded cryo-EM facility (https://www.ed.ac.uk/biology/research/facilities/electron-microscopy) Regular time on macromolecular crystallography and SAXS synchrotron beamlines at Diamond Light Source (https://www.diamond.ac.uk) Regular cryo-EM time on Titan-Krios microscopes at Diamond Light Source (https://www.diamond.ac.uk) and Jeol microscopes at the Scottish Centre for Macromolecular Imaging (https://www.gla.ac.uk/researchinstitutes/iii/cvr/facilities/scmi/) Local provision of high-performance GPU computation for cryo-EM, modelling and molecular dynamics This position provides a unique opportunity for a highly enthusiastic applicant to perform transformative research through an integrative approach that is directed towards the new era of structural biology that address protein assemblies at a cellular scale. The successful candidate will lead this project (including several PhD students), and will be fully supported in applying for postdoctoral research fellowships within the lab, and independent research positions at the end of the postdoc. In suitable cases, at least part of the project, or a new project to be started during the employment, could be taken by the successful candidate as the basis for their future research career. Please see the following manuscripts for examples of our previous work: https://www.nature.com/articles/s41594-021-00636-z https://www.nature.com/articles/s41594-018-0078-9 https://www.nature.com/articles/s41467-018-07794-7 https://www.science.org/doi/10.1126/sciadv.abb1660 https://elifesciences.org/articles/60175 Full publication list available at https://www.ed.ac.uk/profile/dr-owen-davies The advert for the position is available via the following link: https://www.jobs.ac.uk/job/CRX346/postdoctoral-research-associate-in-the-st… The application deadline is 6th September, and candidates should apply by following the 'apply' link on the above advert. Please feel free to contact me directly (Owen.Davies(a)ed.ac.uk<mailto:[email protected]>) for informal discussions and additional information. Best wishes, Owen. Dr Owen Davies Wellcome Senior Research Fellow Wellcome Centre for Cell Biology University of Edinburgh Michael Swann Building Max Born Crescent Edinburgh EH9 3BF United Kingdom The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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Inability to connect the N and C terminal of peptide to form a peptid bond of a circular peptide structure
by Jiang Xu 14 Aug '22

14 Aug '22

Hello Guys, I have a circular peptide structure solved from Xtal. The peptide is actually a circular peptide that has the N terminal and C terminal joined together by a peptide bond. When refining the structure, I had a problem getting the C-N terminal (between G34 and S2) joined together by the peptide bond. I even made a link between the C terminal carbon atom and N terminal N atom in coot and used this model as the input model to do the refinement using Phenix.refine. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoid forming a bond between the C atom and the N atom. So, how can I solve this problem? Thank you, Best regards, Jiang Lin Chen Lab University of Southern California P.S. coot manually made link between the C and N terminal [image: unnamed.jpg] After refinement [image: unnamed (1).jpg]

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Postdoc Opportunity - Multidataset X-ray Crystallography, Computational Structural Biology, & Protein Allostery - Upper Manhattan, New York City
by Keedy, Daniel 09 Aug '22

09 Aug '22

Hello Phenix community, The Keedy Lab at the CUNY Advanced Science Research Center in New York City has a funded Postdoctoral Scholar position available immediately. We seek applications from individuals with experience in computational biology, computer science, software development, biochemistry, biophysics, or a related area. Details of research projects and career training will be tailored to the goals of the successful applicant. Research: The Keedy Lab is interested in the interplay between protein sequence, conformational heterogeneity, and biological function. Using a unique combination of avant-garde computational and biophysical approaches, we aim to elucidate the conformational ensembles of proteins and to understand how they are shifted by perturbations, including temperature, pressure, mutations, ligands, protein:protein interactions, to control biological function. The successful applicant for this open position will join these efforts by developing and using new computational approaches to exploit families of related structures, extract hidden signatures of conformational heterogeneity, and explore how changes to amino acid sequence rewire protein allosteric networks. Location: The CUNY Advanced Science Research Center (https://asrc.gc.cuny.edu) is a cutting-edge research institution, perched atop a hill overlooking Harlem in New York City. Alongside its sister research building, the City College of New York’s Center for Discovery and Innovation, the ASRC sits in an oasis of green amidst upper Manhattan. The ASRC Structural Biology Initiative features eight tenure-track and research-track faculty members, pursuing diverse research problems using X-ray diffraction, mass spectrometry, cryo-EM, NMR, solution biophysics, and advanced microscopy. The ASRC is immediately adjacent to the New York Structural Biology Center, a consortium of CUNY and eight other New York academic institutions with world-class facilities, and is just 70 miles from Brookhaven National Laboratory, featuring the National Synchrotron Light Source II – the brightest synchrotron light source in the United States. You can read more about the Keedy lab here: https://keedylab.org Please officially apply for the position here: https://www.rfcuny.org/careers/postings?pvnID=RC-2207-004956 You may also email me directly to ask questions or discuss. I look forward to hearing from you! Best regards, Daniel Keedy — Daniel A. Keedy, PhD Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry, Biology, and Chemistry PhD Programs, CUNY Graduate Center dkeedy(a)gc.cuny.edu<mailto:[email protected]> | https://keedylab.org | 919-724-6064

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Naming/refining glycosylation
by Tynan Young 09 Aug '22

09 Aug '22

Hi all, I am having issues with naming of glyco- groups and refining my glycosylated EM structure in Coot. I have noticed that many models use the same chain ID for the glyco- groups as the chain ID they are attached to (i.e. NAG/B/1301 would be linked to ASN/B/121). When working with the model in Coot, I would like to refine only the ASN 121 and the NAG 1301 attached to it. However, due to the naming of the glyco- group, Coot will refine residues 121-1301. Not only is this very time-consuming, but it will disrupt the rest of the model - which I do not want to do. If I change the chain ID of the glyco- group to an altogether different chain ID, then I can no longer refine both the side chain and the glyco- group. Is there some naming scheme that avoids this issue? Any help is greatly appreciated. Thank you. Tynan ---------------------------------------------------------------------- ------------------------------------------------------------ -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ------------------------------------------------------------

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Phenix and coot
by Cygler, Miroslaw 08 Aug '22

08 Aug '22

Hi, The phenix connection to graphics software stopped working on my laptop after a refine job got suspended and I had to force quit the program (abort function did not work). Now when I run refinement the coot does not start automatically. How can I reconnect phenix with coot and pymol? Thanks, Mirek

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Drug Discovery Scientist opening Vanderbilt University
by Harp, Joel M 13 Jul '22

13 Jul '22

Drug Discovery Scientist Position An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a candidate with experience in the field of protein x-ray crystallography or NMR. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus but not required. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]> The Vanderbilt campus is located in Nashville, Tennessee. Also known as Music City, Nashville is a fast growing and dynamic environment with plenty of cultural attractions and opportunities for outdoor recreation. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscm…>

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Postdoctoral position in drug discovery
by Harp, Joel M 12 Jul '22

12 Jul '22

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]>

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Reminder: Phenix user workshop at the ACA2022 in Portland
by Dorothee Liebschner 05 Jul '22

05 Jul '22

Dear Colleagues, The Phenix developers will be holding a day-long satellite workshop on July 29th, prior to the ACA meeting in Portland, Oregon. This Phenix user workshop will focus on using predicted models for crystallography and cryo-EM. *Please note: Registration closes on July 8th!* The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. Topics will cover aspects of macromolecular structure determination in Phenix. For registration, see the ACA 2022 website: https://www.acameeting.com/aca-wk2. You need to register for the main meeting in order to participate in the workshop. This is an in-person workshop (no hybrid option). Lecturers: Pavel Afonine, Dorothee Liebschner, Billy Poon, Tom Terwilliger Looking forward to seeing you there! The Phenix team Detailed Program: 8:00 Welcome: Introduction to Phenix, Introduction to the GUI, set up Phenix 8:45 Overview -- Strategy for X-ray or Cryo-EM structure determination using AlphaFold models (lecture) 9:15 Predicting your structure with AlphaFold and trimming it with ProcessPredictedModel (demo) 9:45 Solving an X-ray structure automatically by MR with PredictAndBuild (demo with pre-computed data) 10:15 Break 10:45 Evaluating X-ray data with Xtriage 11:00 Xray refinement (lecture) 11:30 Xray refinement with AlphaFold reference models (demo) 12:00 Lunch 13:00 Ligands (lecture & demo) 13:30 Cryo-EM Data evaluation with Mtriage (short lecture & demo) 13:45 Cryo-EM map manipulations, map improvement with LocalAnisoSharpen and ResolveCryoEM (demo) 14:30 Break 15:00 Automatic cryo-EM map interpretation with PredictAndBuild (demo with pre-computed data) 15:30 Cryo-EM refinement (lecture and demo) 16:00 Model validation (lecture & demo) 16:30 Q&A 16:50 finish: workshop survey and wrap up -- 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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mmCIF output by phenix.refine
by Mark Saper 30 Jun '22

30 Jun '22

Why does .CIF file output by phenix.refine contain all of the -h -k -l reflections. The Bijvoet reflections are already contained in the _refln.pdbx_F_minus column of the +h +k +l reflections. When OneDep at PDB reads in these files, it finds ‘?’ in about half of the reflections, and assigns them a status of ‘x': Warning: (data block=1): 36739 reflections have status assigned as '?' (changed to 'x') Warning: (data block=1): 36739 reflections have wrong status. Not in list(o,f,x,-,<,h,l) Is this the correct behavior? My space group is 19. Thanks, Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505

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3x4 matrix for wwPDB deposition
by Christian Tüting 28 Jun '22

28 Jun '22

Hi Phenix Dev team and mailing list recipients, i have a question regarding the 4x3 matrix in the wwPDB deposition assembly tab. I am wondering, if there is an easier way, than what I am currently doing. This is my current workflow: # get the map symmetry phenix.map_symmetry symmetry=O map.mrc # apply symmetry on monomer phenix.apply_ncs mono.pdb symmetry_from_map.ncs_spec # get biomt from complex phenix.find_ncs apply_ncs.pdb # isolate wwPDB deposition 3x4 matrix awk '{print substr($0, 25)}' find_ncs.biomt > 3x4_matrix And this feels a bit redundant, as I already have the symmetry operation directly from the beginning, but the monomeric localization is missing. Is there an easier way to get the 3x4 matrix? This is still fast, so this is fine, but maybe there is an easier, single line solution. Best Christian

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Running phenix into a M1 apple processor
by Armando Albert 24 Jun '22

24 Jun '22

Dear all, Is there any version of phenix for the new M1 apple processors? Thank you Armando

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Building DNA into the cryo-EM map density
by Yangqi Gu 21 Jun '22

21 Jun '22

Dear PHENIX users and developers, I am currently building a model for a cryo-EM map of a helical complex. I could build the protein easily into the map. However, the map also contains a long chain of DNA density, I am wondering what could be the best way to build this DNA model? I have no previous experience building models with a DNA complex, therefore any suggestion would be helpful! Best. Yangqi -- Yangqi Gu Ph.D. Yale University, West Campus

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ACA hotel block closing June 17
by Anna Gardberg 14 Jun '22

14 Jun '22

Dear Colleagues, The ACA annual meeting in Portland is fast approaching. The meeting will be held from July 29 - August 3, 2022. The hotel room block at the Marriott Downtown Waterfront will be closing on June 17th. Book your room today <https://book.passkey.com/event/50263127/owner/3508/home>! Register for the meeting <https://www.acameeting.com/registration-info> and consider taking one of the workshops <https://www.acameeting.com/workshops> on July 29. WK1: Applications of Small Angle Scattering to Structural Biology: An Introduction WK2: Crystallographic and cryo-EM Structure Solution with Phenix WK3: Cryo-Electron Tomography: State of the Art Methods WK4: Hands-on Single-Particle Cryo-EM Data Analysis with Cryo EDU WK5: CryoEM Sample Preparation Training using Center Merit Badges WK6: Advanced Software Tools for Single Crystal Diffraction WK7: Visualizing Structure WK8: Microcrystal Electron Diffraction (MicroED) If you are already registered for the proximally located M&M conference, you can register for the ACA workshops and/or an ACA one day pass <https://acas.memberclicks.net/index.php?option=com_mcform&view=ngforms&id=2…> . We look forward to seeing you in Portland! The 2022 Annual Meeting Committee

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phenix.douse, resampled map?
by Guenter Fritz 12 Jun '22

12 Jun '22

Dear Pavel, dear all, I was running phenix.douse on a map from resolve. It works very nicely. As far as I understand phenix.douse generates a resampled map with finer grid for water picking. Is there an option to write this resampled map out? Best regards, Guenter

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high R-value with resolve_cryo_em
by Daniel Larsson 10 Jun '22

10 Jun '22

Hi all, I tried to do density modification using the resolve_cryo_em tool. The resolution improves quite a lot from around 2.60 to around 2.35 and the density looks significantly better than the autorefined original map. However, the R-values is close to 0.5, which seems very high. How should the R-value generated by this tool be interpreted? It is very poorly documented and not mentioned in the paper or on the manual page, but Tom Terwilliger mentioned in a workshop that “low number is good” and “point two-four is a very good number, point five is not a good number”, which makes me worried. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Postdoctoral position in Manchester
by Harshwardhan Poddar 08 Jun '22

08 Jun '22

Hi everyone, There is a PostDoc position available in the laboratory of Prof Nigel Scrutton based at Manchester Institute of Biotechnology. This is an exciting opportunity to characterise some newly discovered light-sensitive proteins using time-resolved structural techniques. More details can be found here- Research Associate in Structural Biology : Manchester Institute of Biotechnology (MIB) | | | | | | | | | | | Research Associate in Structural Biology : Manchester Institute of Biotechnology (MIB) | | | | Best Harshwardhan

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Structural Biology position at Odyssey Therapeutics (Boston MA)
by Chip Lesburg 06 Jun '22

06 Jun '22

Opportunity for a Senior/Principal Scientist at Odyssey Therapeutics in Boston MA. We are seeking a highly motivated and skilled Structural Biologist to join the Odyssey team at our site in Boston where you will be a key contributor to the structural enablement of pipeline discovery projects. You will employ cutting-edge structural techniques such as cryo-EM and X-ray crystallography in a cost-effective, efficient manner. You will use your expertise to better understand mechanisms of action and structural aspects of protein-protein and protein-ligand interactions, and to guide protein therapeutic design. You will oversee the production of quality proteins in support of biophysical and structural analyses. Working closely within therapeutic project teams, you will determine and communicate the structures of both protein-small molecule complexes and multiprotein complexes. In this primarily lab-based role, you will be a key contributor to the application of internal and external resources and capabilities necessary to drive biophysics and structural biology efforts. More information, including responsibilities and desired skills, can be found at: https://boards.greenhouse.io/odysseytherapeutics/jobs/4538034004 Chip Lesburg [cid:153156_edd5022b-de61-48a6-bf68-1a41de35ba89.png] Charles Lesburg Vice President, Structural Biology M 908-265-2064 301 Binney Street, Cambridge, MA 02142 odysseytx.com This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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Problem with rebuild_predicted_model
by Andrei Moiseenko 04 Jun '22

04 Jun '22

Dear all, I am trying to build the model with Alphafold2 using Dock and Rebuild and encountered some issue with rebuild_predicted_model. It does not rebuild the model telling that: "Unable to morph model...may not match exactly in chain ID or residue numbers. No morphed model obtained... No docked model to work with." I use the model predicted with Alphafold2 google colab and the cryoem map with 3.5A resolution boxed around the protein of interest. The process_predicted_model and dock_predicted_model run successfully, giving the single-chain model which nicely fits into the map (40 of 300 residues are excluded due to low LDDT). The chain ID in the docked model is indeed different from predicted model: the predicted model has one chain A, but the docked one has A1. However, manually changing the chain ID either in the predicted or in the docked model does not resolve the issue. Manual runs of rebuild_predicted_model also fail with the same result. Tried it with models and maps for different proteins, tried both on Linux and Windows - it gives the same output (Phenix 1.20.1.-4487). Please, find the log attached. I am seeking for any advice on resolving this problem. Best regards Andrey Moiseenko Electron Microscopy Lab @ Biology Department Moscow State University <mailto:[email protected]> postmoiseenko(a)gmail.com skype: callmoiseenko

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custom planar restraints ?
by Guenter Fritz 30 May '22

30 May '22

Dear all, is it possible to define custom planar restraints, let's say atoms A,B,C,D from residue Z should stay in a plane. Best regards, Guenter

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Phenix user workshop at the ACA2022 in Portland
by Dorothee Liebschner 24 May '22

24 May '22

Dear Colleagues, The Phenix developers will be holding a day-long satellite workshop on July 29th, prior to the ACA meeting in Portland, Oregon. This Phenix user workshop will focus on using predicted models for crystallography and cryo-EM The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. Topics will cover aspects of macromolecular structure determination in Phenix. For registration, see the ACA 2022 website: https://www.acameeting.com/aca-wk2 . Lecturers: Pavel Afonine, Dorothee Liebschner, Billy Poon, Tom Terwilliger Looking forward to seeing you there! The Phenix team Detailed Program: 8:00 Welcome: Introduction to Phenix, Introduction to the GUI, set up Phenix 8:45 Overview -- Strategy for X-ray or Cryo-EM structure determination using AlphaFold models (lecture) 9:15 Predicting your structure with AlphaFold and trimming it with ProcessPredictedModel (demo) 9:45 Solving an X-ray structure automatically by MR with PredictAndBuild (demo with pre-computed data) 10:15 Break 10:45 Evaluating X-ray data with Xtriage 11:00 Xray refinement (lecture) 11:30 Xray refinement with AlphaFold reference models (demo) 12:00 Lunch 13:00 Ligands (lecture & demo) 13:30 Cryo-EM Data evaluation with Mtriage (short lecture & demo) 13:45 Cryo-EM map manipulations, map improvement with LocalAnisoSharpen and ResolveCryoEM (demo) 14:30 Break 15:00 Automatic cryo-EM map interpretation with PredictAndBuild (demo with pre-computed data) 15:30 Cryo-EM refinement (lecture and demo) 16:00 Model validation (lecture & demo) 16:30 Q&A 16:50 finish: workshop survey and wrap up -- 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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Exciting post-doc position available on DNA transcription and conjugation at the ALBA synchrotron
by Roeland Boer 17 May '22

17 May '22

Dear fellow structural biologists, I would appreciate it if you could forward this message to anyone that might be interested. We are looking for an enthusiastic and motivated early-career postdoc to study the structural aspects of auxin-dependent transcription regulation in plants, and/or plasmid conjugation in gram-positive bacteria at the ALBA synchrotron (Barcelona, Spain). The project is a continuation of the research lines of a highly successful research group, including publications in Cell (10.1016/j.cell.2013.12.027), Nature Communications (10.1038/s41467-020-16032-y), Nucleic Acids Research (10.1093/nar/gkaa540 and 10.1093/nar/gky996), Nature Plants (10.1038/s41477-020-0662-y) and PNAS (10.1073/pnas.2009554117). At the ALBA synchrotron, exciting times lie ahead for structural biologists. Recently, a new EM facility has been built and is being commissioned at the moment. In addition, an upgrade of the storage ring will come to fruition in the coming 5-10 years. Furthermore, a microfocus beamline is under construction that will be open to friendly users in the year to come. These instruments will complement the macromolecular crystallography, SAXS, infrared microscopy and X-ray microscopy beamlines currently in operation. The facility is located near Barcelona, which is a great city to live and work. For inquiries, please contact me at rboer(a)cells.es. To apply, please check the following page: https://public.cells.es/jobs/#!/jobs/postdoctoral-researcher-position-minec… Best, Roeland. -- <https://www.albasynchrotron.es/en/> Roeland Boer XALOC beamline- Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Carrer de la Llum 2-26 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <https://www.albasynchrotron.es/en/about/coming-to-alba> (+34) 93 592 4333 www.albasynchrotron.es <http://www.albasynchrotron.es>| rboer(a)cells.es <mailto:[email protected]> | legal notice <https://www.albasynchrotron.es/en/about/legal-notice> / avís legal <https://www.sincrotroalba.cat/ca/que-es-alba/avis-legal> / aviso legal <https://www.sincrotronalba.es/es/que-es-alba/aviso-legal> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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problem in cif file from Real-space refinement
by princeadam＠163.com 14 May '22

14 May '22

Dear all, I used the "Get PDB validation report"to refine my protein-ligand complex. The cif file got from "Get PDB validation report" was put into "Prepare model for PDB depositon" and then I used "Get PDB validation report" to see the validation report. It's a pity I got the following error message from "Get PDB validation report": The PDB server reports a failure with you data. Please check that your input files following the CIF specifications. However, if I use the cif file from phenix.refine with the same procedure, I got the validation reports normally. Does anyone has similar problem? I am using Phenix 1.20.1-4487. Thanks a lot for the help. Best Liu

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problem in cif file from Real-space refinement
by princeadam＠163.com 14 May '22

14 May '22

Dear all, Sorry, I made a mistake in the former email. I used the "real space refinement"to refine my protein-ligand complex. The cif file got from "real space refinement" was put into "Prepare model for PDB depositon" and then I used "Get PDB validation report" to see the validation report. It's a pity I got the following error message from "Get PDB validation report": The PDB server reports a failure with you data. Please check that your input files following the CIF specifications. However, if I use the cif file from phenix.refine with the same procedure, I got the validation reports normally. Does anyone has similar problem? I am using Phenix 1.20.1-4487. Thanks a lot for the help. Best Liu

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Error during phenix refine
by Shisler, Krista 12 May '22

12 May '22

Dear All, I ran Phaser-MR on my data (which I analyzed with xds) and was able to obtain a model with an TFZ score of 10.8. However, when I try to refine, I am getting an error message saying "cctbx Error: merge_equivalents_exact: incompatible flags for hkl = (-71, 39, 62) (mismatch between Friedel mates)." Is there a way to edit these flags or do I need to analyze my data again? Thank you! Krista

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