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Staff Scientist opportunity in "Single Molecule Biophysics" at Human Technopole in Milan, Italy
by Sebastiano Pasqualato 20 Jan '22

20 Jan '22

Dear all, another job post from the newly established life science Institute of Milan, Italy, Human Technopole (http://www.humantechnopole.it/en/ <http://www.humantechnopole.org/>) We are looking for a Staff Scientist to establish and manage a Single Molecule Biophysics Platform as a part of an ongoing collaboration with Lumicks. We are looking for persons with proven track record in single-molecule studies, with specific experience with Lumicks optical tweezers (C-trap and M-trap). The successful candidate will work in close collaboration with the Scientists of the Structural Biology Research Centre of Human Technopole (https://humantechnopole.it/en/research-centres/structural-biology/ <https://humantechnopole.it/en/research-centres/structural-biology/>), and their platform will be part of a larger number of research facilities and platforms, such as the Cryo-EM facility (https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ <https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>). More details, and how to apply can be found at the following link: https://careers.humantechnopole.it/o/staff-scientist-single-molecule-biophy… <https://careers.humantechnopole.it/o/staff-scientist-single-molecule-biophy…> Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager

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Structural Biology Cryo-EM TT Asst. Professor at University of Nebraska
by Alex Vecchio 17 Jan '22

17 Jan '22

Dear PhenixBB Community, I would like to bring your attention to a Tenure-track faculty position at the rank of Assistant Professor in the Department of Biochemistry at the University of Nebraska-Lincoln (UNL). We are looking for candidates with research programs studying the structural biology of macromolecules relevant to human health or disease using cryo-EM. UNL has established a state-of-the-art cryo-EM facility that will house a Glacios 200 keV Cryo-TEM equipped with a Falcon 4i detector, a Selectris energy filter, and have capabilities for microED of crystalline samples. The candidate will be part of the Nebraska Center for Integrated Biomolecular Communication (NCIBC), an NIH-funded COBRE center, and have the opportunity to collaborate with other researchers spanning several departments across the UNL. For more information, please read our ad in Science Careers, HERE <https://jobs.sciencecareers.org/job/580579/assistant-professor-structural-b…> . To apply, please visit the UNL Employment Website, HERE <https://employment.unl.edu/postings/76851>. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* *University of Nebraska–Lincoln* *Department of Biochemistry* *Center for Integrated Biomolecular Communication* 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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regarding number of unique reflections
by Viney Singh 14 Jan '22

14 Jan '22

Dear all, First of all sorry for the novice question. I *processed* one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True. The number of unique reflections I got: *17,000* I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations. Now, when I am trying to* refine *the structure in Phenix, the structure is being refined against *32,300* reflections with *3230* reflections for Rfree calculation. Looks like refinement is treating Friedel's pair as two different reflections. When I am trying to upload PDB on rcsb, on the refinement tab, the number of reflections used for refinement and Rfree calculations are shown as 32,300 and 3220 respectively, while in the validation report, no. of reflections used for Rfree calculation are shown as *1700*. I would really appreciate if someone can guide me to resolve this discrepancy. Thanks in advance. Viney

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Staff Scientist opportunity in "Structural Proteomics" at Human Technopole in Milan, Italy
by Sebastiano Pasqualato 14 Jan '22

14 Jan '22

Dear all, the newly established Human Technopole Institute, based in Milan, Italy (http://www.humantechnopole.it/en/ <http://www.humantechnopole.org/>) is looking for a Staff Scientist to manage the Structural Proteomics Facility. We are looking for persons with proven track record in high-resolution MS-based proteomics, with specific experience in cross-linking- (XL) and native- MS. Structural proteomics technologies will be closely integrated with the Science Groups of the Structural Biology Research Centre of Human Technopole (https://humantechnopole.it/en/research-centres/structural-biology/ <https://humantechnopole.it/en/research-centres/structural-biology/>), and will be part of a larger number of research facilities and platforms, such as the Cryo-EM facility (https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ <https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>) More details, and how to apply can be found at the following link: https://careers.humantechnopole.it/o/staff-scientist-to-manage-a-structural… <https://careers.humantechnopole.it/o/staff-scientist-to-manage-a-structural…> Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager

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Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability
by Oliver Clarke 13 Jan '22

13 Jan '22

Hi, Just to add my two cents, I agree this would be really useful for a lot of folks. Analysis of continuously distributed variability is very common these days in cryoEM, and having a way to jointly refine an ensemble of models against a series of maps would be very handy. Cryodrgn, 3D-VA in cryosparc, ManifoldEM, multibody refinement in relion - there are many tools now for generating a series of density maps potentially corresponding to conformational modes, so having the capacity in phenix to refine models against each map would be very helpful. Cheers Oli > > > Message: 1 > Date: Wed, 12 Jan 2022 10:36:27 +0100 > From: vincent Chaptal <vincent.chaptal(a)ibcp.fr> > To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se>, Pavel Afonine > <pafonine(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] refinement of an ensemble of structures -> > cryoEM variability > Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3(a)ibcp.fr> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi Guillaume, > > thanks for the backup. > It's exactly my feeling also. > > Best > Vincent > > Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?: >> Hi, >> >> I am guessing what we are talking about here are the maps generated by >> cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D >> Variability Analysis: Resolving continuous flexibility and discrete >> heterogeneity from single particle cryo-EM.?Journal of Structural >> Biology: 107702 https://doi.org/10.1016/j.jsb.2021.107702 >> >> But this is not the only program that generates series of maps to >> describe continuous heterogeneity from single-particle cryoEM images, >> see also cryoDRGN:?Zhong ED, Bepler T, Berger B & Davis JH (2021) >> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using >> neural networks.?Nature Methods: 1?10 >> https://doi.org/10.1038/s41592-020-01049-4 >> >> Except some ideally rigid particles like apoferritin, pretty much >> everything shows some degree of flexibility that generates continuous >> heterogeneity in cryoEM images. So, my feeling is that a user-friendly >> program to fit a series of models (ideally, auto-generated from a >> single starting model) to a map series is probably going to be a >> standard requirement pretty soon for typical single-particle cryoEM >> projects. >> >> Cheers, >> >> Guillaume >> >> >>> On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine(a)lbl.gov> wrote: >>> >>> Hi Vincent, >>> >>> this looks like a very specialized task that I've never heard of >>> before! We can add a tool to do that if this becomes something that >>> more than one person does more than once. Meanwhile, a simple script >>> in a language of your?preference (python, linux shell, etc) should do >>> the job. I can help with a script if needed, let me know! >>> >>> Also.. just curious -- what is "3D variability of this map"? Is this >>> one map that is a composition of several map or an ensemble of maps? >>> >>> Pavel >>> >>> On 1/11/22 01:48, vincent Chaptal wrote: >>>> Hi Phenix-ers, >>>> >>>> I thought to ask for something that I believe you have already >>>> implemented, but I'm not sure of the best tool to use. >>>> >>>> I have a cryoEM map where I refine my "high resolution" structure. I >>>> also have the 3D variability of this map that shows?several maps >>>> varying around the consensus high-res map. I want to refine an >>>> ensemble (20) of structures, one for every 20?maps around the >>>> consensus map. >>>> Is there a tool in phenix to do this? >>>> >>>> I could refine individually the high-res structure into each map >>>> incrementally; since every map differs a little from the?original >>>> one, Real-space-refinement could move the structure a little at a >>>> time. Then I could combine all the PDBs in an?ensemble? >>>> A tool to refine variability would be very useful. Input could be a >>>> PDB and an ensemble of maps, and output would be all the?PDBs combined? >>>> >>>> Thank you. >>>> >>>> All the best >>>> Vincent >>>> >>>> >>>> -- >>>> Vincent Chaptal, PhD >>>> Director of GdR APPICOM >>>> Drug Resistance and Membrane Proteins Lab >>>> >>>> MMSB -UMR5086 >>>> 7 passage du Vercors >>>> 69007 LYON >>>> FRANCE >>>> +33 4 37 65 29 01 >>>> http://www.appicom.cnrs.fr >>>> http://mmsb.cnrs.fr/en/ >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> Page Title >> >> >> >> >> >> >> >> N?r du har kontakt med oss p? Uppsala universitet med e-post s? >> inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om >> hur vi g?r det kan du l?sa h?r: >> 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 > > -- > > Vincent Chaptal, PhD > > Director of GdR APPICOM > > Drug Resistance and Membrane Proteins Lab > > > MMSB -UMR5086 > > 7 passage du Vercors > > 69007 LYON > > FRANCE > > +33 4 37 65 29 01 > > http://www.appicom.cnrs.fr > > http://mmsb.cnrs.fr/en/ > >

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Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability
by Oliver Clarke 13 Jan '22

13 Jan '22

I guess it isn't all that different. If you run all jobs naively starting from a single model corresponding to the overall reconstruction, depending on the magnitude of the conformational changes the maps at either end of the series may be outside the radius of convergence of phenix.real_space_refine (with default parameters). Some way to initially perturb a single model to more-or-less match the series of maps would be useful (maybe morphing in real_space_refine will already work for this?). This could probably be scripted, but having it built into phenix would be useful I think. Oli > Date: Thu, 13 Jan 2022 09:26:50 -0800 > From: James Holton <jmholton(a)lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] refinement of an ensemble of structures -> > cryoEM variability > Message-ID: <92b5f0e3-c4b1-59f9-1c38-50fffcda0bb1(a)lbl.gov> > Content-Type: text/plain; charset=UTF-8; format=flowed > > How is that different from running parallel jobs of n models against n maps? > > On 1/13/2022 8:17 AM, Oliver Clarke wrote: >> Hi, >> >> Just to add my two cents, I agree this would be really useful for a lot of folks. Analysis of continuously distributed variability is very common these days in cryoEM, and having a way to jointly refine an ensemble of models against a series of maps would be very handy. Cryodrgn, 3D-VA in cryosparc, ManifoldEM, multibody refinement in relion - there are many tools now for generating a series of density maps potentially corresponding to conformational modes, so having the capacity in phenix to refine models against each map would be very helpful. >> >> Cheers >> Oli >> >>> >>> Message: 1 >>> Date: Wed, 12 Jan 2022 10:36:27 +0100 >>> From: vincent Chaptal <vincent.chaptal(a)ibcp.fr> >>> To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se>, Pavel Afonine >>> <pafonine(a)lbl.gov> >>> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> >>> Subject: Re: [phenixbb] refinement of an ensemble of structures -> >>> cryoEM variability >>> Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3(a)ibcp.fr> >>> Content-Type: text/plain; charset="utf-8"; Format="flowed" >>> >>> Hi Guillaume, >>> >>> thanks for the backup. >>> It's exactly my feeling also. >>> >>> Best >>> Vincent >>> >>> Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?: >>>> Hi, >>>> >>>> I am guessing what we are talking about here are the maps generated by >>>> cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D >>>> Variability Analysis: Resolving continuous flexibility and discrete >>>> heterogeneity from single particle cryo-EM.?Journal of Structural >>>> Biology: 107702 https://doi.org/10.1016/j.jsb.2021.107702 >>>> >>>> But this is not the only program that generates series of maps to >>>> describe continuous heterogeneity from single-particle cryoEM images, >>>> see also cryoDRGN:?Zhong ED, Bepler T, Berger B & Davis JH (2021) >>>> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using >>>> neural networks.?Nature Methods: 1?10 >>>> https://doi.org/10.1038/s41592-020-01049-4 >>>> >>>> Except some ideally rigid particles like apoferritin, pretty much >>>> everything shows some degree of flexibility that generates continuous >>>> heterogeneity in cryoEM images. So, my feeling is that a user-friendly >>>> program to fit a series of models (ideally, auto-generated from a >>>> single starting model) to a map series is probably going to be a >>>> standard requirement pretty soon for typical single-particle cryoEM >>>> projects. >>>> >>>> Cheers, >>>> >>>> Guillaume >>>> >>>> >>>>> On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine(a)lbl.gov> wrote: >>>>> >>>>> Hi Vincent, >>>>> >>>>> this looks like a very specialized task that I've never heard of >>>>> before! We can add a tool to do that if this becomes something that >>>>> more than one person does more than once. Meanwhile, a simple script >>>>> in a language of your?preference (python, linux shell, etc) should do >>>>> the job. I can help with a script if needed, let me know! >>>>> >>>>> Also.. just curious -- what is "3D variability of this map"? Is this >>>>> one map that is a composition of several map or an ensemble of maps? >>>>> >>>>> Pavel >>>>> >>>>> On 1/11/22 01:48, vincent Chaptal wrote: >>>>>> Hi Phenix-ers, >>>>>> >>>>>> I thought to ask for something that I believe you have already >>>>>> implemented, but I'm not sure of the best tool to use. >>>>>> >>>>>> I have a cryoEM map where I refine my "high resolution" structure. I >>>>>> also have the 3D variability of this map that shows?several maps >>>>>> varying around the consensus high-res map. I want to refine an >>>>>> ensemble (20) of structures, one for every 20?maps around the >>>>>> consensus map. >>>>>> Is there a tool in phenix to do this? >>>>>> >>>>>> I could refine individually the high-res structure into each map >>>>>> incrementally; since every map differs a little from the?original >>>>>> one, Real-space-refinement could move the structure a little at a >>>>>> time. Then I could combine all the PDBs in an?ensemble? >>>>>> A tool to refine variability would be very useful. Input could be a >>>>>> PDB and an ensemble of maps, and output would be all the?PDBs combined? >>>>>> >>>>>> Thank you. >>>>>> >>>>>> All the best >>>>>> Vincent >>>>>> >>>>>> >>>>>> -- >>>>>> Vincent Chaptal, PhD >>>>>> Director of GdR APPICOM >>>>>> Drug Resistance and Membrane Proteins Lab >>>>>> >>>>>> MMSB -UMR5086 >>>>>> 7 passage du Vercors >>>>>> 69007 LYON >>>>>> FRANCE >>>>>> +33 4 37 65 29 01 >>>>>> http://www.appicom.cnrs.fr >>>>>> http://mmsb.cnrs.fr/en/ >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> Page Title >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> N?r du har kontakt med oss p? Uppsala universitet med e-post s? >>>> inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om >>>> hur vi g?r det kan du l?sa h?r: >>>> 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 >>> -- >>> >>> Vincent Chaptal, PhD >>> >>> Director of GdR APPICOM >>> >>> Drug Resistance and Membrane Proteins Lab >>> >>> >>> MMSB -UMR5086 >>> >>> 7 passage du Vercors >>> >>> 69007 LYON >>> >>> FRANCE >>> >>> +33 4 37 65 29 01 >>> >>> http://www.appicom.cnrs.fr >>> >>> http://mmsb.cnrs.fr/en/ >>> >>>

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refinement of an ensemble of structures -> cryoEM variability
by vincent Chaptal 12 Jan '22

12 Jan '22

Hi Phenix-ers, I thought to ask for something that I believe you have already implemented, but I'm not sure of the best tool to use. I have a cryoEM map where I refine my "high resolution" structure. I also have the 3D variability of this map that shows several maps varying around the consensus high-res map. I want to refine an ensemble (20) of structures, one for every 20 maps around the consensus map. Is there a tool in phenix to do this? I could refine individually the high-res structure into each map incrementally; since every map differs a little from the original one, Real-space-refinement could move the structure a little at a time. Then I could combine all the PDBs in an ensemble? A tool to refine variability would be very useful. Input could be a PDB and an ensemble of maps, and output would be all the PDBs combined? Thank you. All the best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Excellent Opportunity for Postdoc in Ion-Channel Structural Biology
by Pramod Kumar 07 Jan '22

07 Jan '22

Dear Structural Biology Scholars, I would like to bring your attention to an excellent opportunity to unravel the structure-function details of ion-channels as a postdoc. The Grosman lab at the University of Illinois at Urbana-Champaign is actively looking to fill a recent opening of NIH-funded postdoctoral position. The laboratory has an excellent record in combining high-resolution electrophysiology, molecular simulations, and structural biology to address fundamental questions about ion-channel mechanisms. Previous experience with the purification of eukaryotic membrane proteins is a plus and structure determination using single-particle cryo-EM is highly preferred. Salary commensurate with the experience level. The University of Illinois Urbana Champaign is an excellent place for research and life with an easy commute, lower-cost housing, easy access to all needs, and a vibrant community with easily accessible cities like Chicago, Indianapolis, St. Louis. Interested individuals should contact Prof. Claudio Grosman ( grosman(a)illinois.edu) with a CV, a 1–2 page description of previous research, and names and contact information of 2–3 references. Students in their final year of Ph.D. training are also welcome to apply. Recent select publications from the Grosman lab are listed below. A complete list of publications from the Grosman lab can be found on Prof. Claudio Grosman’s NCBI bibliography page ( https://www.ncbi.nlm.nih.gov/myncbi/claudio.grosman.1/bibliography/public <https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/myncbi/claudio.gros…> ). *Recent Select Publications * *· Kumar P, Cymes GD, Grosman C. Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc. Natl. Acad. Sci. USA. 2021;118(23). * *doi: 10.1073/pnas.2100164118 * *· Cymes GD, Grosman C. Signal transduction through Cys-loop receptors is mediated by the nonspecific bumping of closely apposed domains. Proc. Natl. Acad. Sci. USA. 2021;118(14). doi: 10.1073/pnas.2021016118 * *doi: 10.1038/s41467-021-21680-9 * *· Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc. Natl. Acad. Sci. USA. 2020;117(3):1788-1798. * *doi: 10.1073/pnas.1906823117 * -- Pramod Kumar, Ph.D.

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use mr_rosetta to prerefine structure
by Wei Wang 07 Jan '22

07 Jan '22

Dear all, I have a question regarding phenix.mr_rosetta. I manually build a model in Coot, and want to use phenix.mr_rosetta to prerefine the model. I followed the instruction on https://phenix-online.org/documentation/reference/mr_rosetta.html#rebuildin…. Basically, my scenario is like what’s written in NOTE 2: “have a model and just want to run pre-refinement and not anything else”. I noticed that if I put nproc=xx, then the job would eventually output no structures. I checked each subjob and found that they all failed. I suspect this behavior was caused by files overwritten by parallel jobs. When I don’t specify nproc, then there’s no problem. However, in this case, for number_of_prerefine_models=1000, it would take a very long time. I hope I described the behavior clearly. Is there a way of running the prerefine jobs in parallel? Thanks, Wei

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Phenix version 1.20 released
by Paul Adams 06 Jan '22

06 Jan '22

The Phenix developers are pleased to announce that version 1.20 of Phenix is now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.20 version of Phenix include a number of tools to leverage new structure prediction methods: - New tools and methods - Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI - phenix.process_predicted_model: Identify useful domains in AlphaFold model - phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM - phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map using docked domains - phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with cryo-EM map - phenix.model_completion: Connect fragments and fill in gaps based on a map - phenix.rebuild_model: Rebuild a model using a map and keeping connectivity - phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments from PDB - phenix.search_and_morph: SSM search PDB; morph to match target - phenix.fragment_search: Search for a fragment in PDB matching target - phenix.reverse_fragment: Reverse chain direction of a fragment - phenix.superpose_and_morph: SSM or least-squares superpose one model on another; optionally trim and morph to match - phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted model quality - phenix.match_maps: - Bug fix (superposed map was not matching target map) - phenix.real_space_refine: - Symmatry multiprocessing aware individual ADP and occupancy refinement - Multiple changes to improce runtime (for certain refinement strategies) - Make NQH flips symmetry aware - phenix.superpose_pdbs: - Add feature to transform additional models with matrix found with moving model - phenix.dock_in_map: - Allow splitting model into domains based on chain ID from phenix.process_predicted_model - Restraints - GeoStd updated with 12k plus entity restraints files - cis-PRO default updated to EH99 - phenix.fetch_pdb, iotbx.cif_as_mtz: - Bug fix: Multiple datasets with different unit cells in a cif file now preserved as multiple crystals in mtz file. Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.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 ] --

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Postdoc Position at Caltech
by Hoelz, Andre 21 Dec '21

21 Dec '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit an outstanding postdoctoral scientist in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The position is available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu). Selected Recent Publications Bley, C.J., Nie, S., Mobbs, G.W., Petrovic, S., Gres, A.T., Liu, X., Mukherjee, S., Harvey, S., Huber, F.M., Lin, D.H., Brown, B., Tang, A.W., Rundlet, E.J., Correia, A.R., Chen, S., Regmi, S.G., Dasso, M., Patke, A., Palazzo, A.F., Kossiakoff, A.A., Hoelz, A. (2021). BioRxiv (https://doi.org/10.1101/2021.10.26.465790). Petrovic, S., Samanta, D., Perriches, T., Bley, C.J., Thierbach, K., Brown, B., Nie, S., Mobbs, G.W., Liu, X., Hoelz, A. (2021). Architecture of the linker-scaffold in the nuclear pore. BioRxiv (https://doi.org/10.1101/2021.10.26.465796). Lin, D. H., Hoelz, A. (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A., (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D., Stuwe, T., Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A. (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T., Bley, C.J., Thierbach, K., Petrovic, S., Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T., Correia, A., Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A., Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643.

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Query re individual sites (real space)
by Oliver Clarke 21 Dec '21

21 Dec '21

Hi, While refining an X-ray structure using phenix.refine (v1.20-4444), I get the attached table during real-space refinement of coordinates. What are the criteria for selecting the correct weighting factor? I assumed it would be the delta between R/Rfree and/or the clash score, but it doesn't seem to exactly match either in this table (and the same for other iterations of refinement). Is it just incorrectly writing the clash score in the "Accepted refinement result" line? Shouldn't this match the line from the selected weight (here 0.125 so should be 6.1, not 7.1)? Cheers Oli

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Phenix.metal_coordination not working in 1.20-4444
by Oliver Clarke 20 Dec '21

20 Dec '21

Hi, When I try to run phenix.metal_coordination in v1.20-4444 (as phenix.metal_coordination whatever.pdb), I get the attached error. Traceback (most recent call last): File "/Applications/phenix-1.20-4444/build/../modules/elbow/elbow/command_line/metal_coordination.py", line 50, in <module> from metal_coordination_params import master_phil_string ImportError: No module named metal_coordination_params Cheers Oli

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Re: [phenixbb] sequence file error in phenix map-to-model
by Raja Dey 20 Dec '21

20 Dec '21

Hi Sharan, I am getting the same error saying , 'is not a known sequence type'. Also, please see the image enclosed below that tells how the template sequence file should look like. I tried with/without space after '>' sign and getting the same error message. [image: image.png] Any suggestion from anyone would be appreciated. Thanks, Raja On Mon, Dec 20, 2021 at 3:29 PM Sharan Karade <sharankarade(a)gmail.com> wrote: > Hi Raja, > > Try to use the file attached here. I hope it works. > > On Mon, Dec 20, 2021 at 3:27 PM Raja Dey <rddey80(a)gmail.com> wrote: > >> Sorry, the error message is >> D41-st-Trx-sequence.txt is not a known sequence type. >> >> Can someone help solving this problem? >> >> Best regards, >> Raja >> >> On Mon, Dec 20, 2021 at 12:02 PM Raja Dey <rddey80(a)gmail.com> wrote: >> >>> Hi, >>> I am getting an error with the sequence file attached. Could you please >>> tell me what's wrong with this file? The error is enclosed below: >>> Starting phenix >>> on Mon Dec 20 11:45:46 2021 by rdey >>> >>> =============================================================================== >>> >>> Processing files: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found phil, >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> >>> Adding PHIL files: >>> ------------------ >>> >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing files from PHIL: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found real_map, >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> >>> Files not used by program: >>> -------------------------- >>> /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> >>> Final processed PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> data_manager { >>> real_map_files = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> default_real_map = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> phil_files = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> default_phil = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> } >>> input_files { >>> map_file = >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> ncs_file = >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> } >>> reconstruction_symmetry { >>> symmetry = """D2""" >>> } >>> control { >>> nproc = 2 >>> } >>> job_title = """D41-st-Trx-19Dec21""" >>> >>> >>> Starting job >>> >>> =============================================================================== >>> Validating inputs >>> >>> >>> Thanks a lot for your time. >>> Regards, >>> Raja >>> >>> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > -- > Sharan Karade > Postdoc-fellow > IBBR-UMD, 9600 Gudelsky Dr, > Rockville > Maryland 20850 > > >

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sequence file error in phenix map-to-model
by Raja Dey 20 Dec '21

20 Dec '21

Hi, I am getting an error with the sequence file attached. Could you please tell me what's wrong with this file? The error is enclosed below: Starting phenix on Mon Dec 20 11:45:46 2021 by rdey =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found real_map, /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc Files not used by program: -------------------------- /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" default_real_map = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" phil_files = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" default_phil = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" } input_files { map_file = /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt ncs_file = /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec } reconstruction_symmetry { symmetry = """D2""" } control { nproc = 2 } job_title = """D41-st-Trx-19Dec21""" Starting job =============================================================================== Validating inputs Thanks a lot for your time. Regards, Raja

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model shifts after real space refinement
by Ashok Nayak 15 Dec '21

15 Dec '21

Hi, Is there a way to say keep_origin=False in phenix real space refinement. I used it in the command line version of v3958. It didn't take that. There is a model shift after the refinement which I think is because the program brings the map to the origin and hence the refined model as well. Thanks, Ashok -- Post-Doctoral Fellow Department of Biochemistry and Molecular Biology, Sidney Kimmel cancer Center Thomas Jefferson University 1020 Locust Street, JAH Philadelphia, PA, 19107 Phone: 804-661-4620

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Job Opportunities at Surrozen Inc (SFO Bay Area)
by Parthasarathy Sampathkumar 14 Dec '21

14 Dec '21

Dear All, I would like to bring to the attention of suitable candidates the following exciting job opportunities at Surrozen Inc, located in South San Francisco. Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines with a focus on unlocking the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Our vision is to engage the body’s own biological tissue repair mechanisms with our targeted regenerative antibodies, overcoming research and development hurdles that have been previously intractable, and have held back drug development efforts in the promising area of Wnt biology. *Research Associate/Senior Research Associate, Biochemistry and Biophysics:* https://apply.workable.com/surrozen/j/ACBA0B0D96/ *Scientist, Protein Sciences: * https://apply.workable.com/surrozen/j/DF4518083F/ *Research Associate, Protein Purification:* https://apply.workable.com/surrozen/j/7D64A01556/ Many Thanks, Best Wishes, Partha Sampathkumar PhD Principal Scientist Surrozen Inc Email: partha(a)surrozen.com

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NIH-funded Postdoc, Membrane Protein Structural Biology
by Alex Vecchio 14 Dec '21

14 Dec '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a Ph.D., with experience in membrane proteins and/or crystallography. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via an NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-nih-fun…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* *University of Nebraska–Lincoln* *Department of Biochemistry* *Center for Integrated Biomolecular Communication* 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Ligand CIF file in real space refinement
by Fadini, Alisia 06 Dec '21

06 Dec '21

Hello, I am trying to use phenix.real_space_refine to improve the fit between my protein's ligand and the electron density. I include a CIF file that has worked well for reciprocal space refinement, made through JLigand. It seems to me that the CIF file is read properly, it does not produce errors and the restrains are stated correctly in the output .cif file that includes all protein + ligand atoms. However, the output pdb shows a distorted ligand, where specific bond angles and bond lengths have been modified past what should be allowed by the restrains. Any insights on how to improve/the causes of this effect would be very welcome! My command is : phenix.real_space_refine model.pdb map.ccp4 ligand.cif resolution=1.63 Thank you, Alisia

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phenix installation problem
by princeadam＠163.com 03 Dec '21

03 Dec '21

Dear all I tried to install Phenix on my virtual machine(Ubuntu) in win11. And got the following error message. ========================================================================== Phenix Installation version: 1.19.2-4158 machine type: intel-linux-2.6-x86_64 OS version: 5.11.0-40-generic destination: /usr/local/phenix-1.19.2-4158 # of processors: 1 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 245, in <module> installer(sys.argv[1:]).install() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.19.2-4158/conda_base/bin/python /usr/local/phenix-1.19.2-4158/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.19.2-4158/build --command_version_suffix 1.19.2-4158 phenix phaser solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 I searched phenixbb, and got the similar information from http://www.phenix-online.org/pipermail/phenixbb/2015-November/022456.html It's a pity , that the answer was not suiable for me. I have root access to write to usr/local. And under /usr/local/phenix-1.19.2-4158 , I can see four folders:build, conda_base, doc, modules. Any one has suggestions? all the best Adam

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opportunity for experienced crystallographer
by Mooers, Blaine H.M. (HSC) 30 Nov '21

30 Nov '21

Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Assistant Professor of Research level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography. The candidate will not be expected to write grant applications. Pluses in a candidate's background include experience with membrane protein purification and LCP crystallization, experience with Cyro-EM, or experience with other structural biology methods like microED, SAXS, SANS, XAFS, NMR, or XFELS. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The BSC has contributed to the awarding of 23 million dollars in grant funding and 33 publications in the past nine years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC will be a vital part of a new Center for Therapeutic Science. The center will coordinate and foster the drug development pipeline with the BSC playing a central role in structure-based drug design. The LBSF will be working closely with Dr. Matt Hart (https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1), Director of the newly established Center for High Throughput Screening. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer. Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at http://ouhsc.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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iotbx.merging_statistics on Python 3: too memory consuming
by Martin Malý 29 Nov '21

29 Nov '21

Dear PHENIX & CCTBX developers and users, I tried to calculate merging statistics with CCTBX tools using Python 3. I realized that the memory requirements are much higher comparing with Python 2... I closed all programs firstly so I had just 1.6 GB RAM used of 7.6 GB total RAM. Then I ran these two lines of code in the cctbx.python shell: import iotbx.merging_statistics i_obs = iotbx.merging_statistics.select_data(file_name="XDS_ASCII.HKL", data_labels=None) Python 2.7: The RAM usage went to 4.8 GB and then I was able to calculate merging statistics. Python 3.7: The module import was successful. Then the RAM usage went to total 7.6 GB and then the process was killed by the operating system (CentOS 7). Please, do you have any suggestion how to use this module "more carefully" and save memory? Thank you! Best regards, Martin Malý ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Job vacancy: Institute Research Investigator within the Therapeutics Discovery Division at MD Anderson Cancer Center
by Leonard,Paul G 18 Nov '21

18 Nov '21

Hi, The Structural Chemistry group, within the Therapeutics Discovery Division of MD Anderson Cancer Center is looking for a highly motivated individual with a strong background in structural biology, using X-ray crystallography and/or single particle cryo-EM to determine high resolution structures of proteins and protein complexes. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for the treatment of cancer or neurodegenerative diseases. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery. The structural chemistry group provides structural biology support for several drug discovery programs in our pipeline, spanning from early stage drug discovery through lead optimization. For a full job description and to submit an application please use the following link... https://jobs.mdanderson.org/search/jobdetails/institute-research-investigat… kind regards, Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Research Associate position in structural biology at Takeda in San Diego
by L Qin 17 Nov '21

17 Nov '21

Dear PHENIX user mailing list members, The Structural Biology group at Takeda Pharmaceuticals in San Diego California has an open position for a Research Associate. I invite interested candidates to apply through the following link: https://www.takedajobs.com/job/san-diego/research-associate-structural-biol… Please feel free to contact me for further information. Best regards, Ling Ling Qin PhD Structural Biology Takeda Development Center Americas 9625 Towne Centre Dr, San Diego, CA 92121 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MizzouForward faculty hiring campaign
by Tanner, John J. 17 Nov '21

17 Nov '21

Dear Colleagues: The University of Missouri has initiated a major faculty hiring campaign, called MizzouForward, which intends to hire 150 new faculty members over the next 5 years. Successful candidates must be research leaders with a passion for collaboration and a proven track record of active, external research funding, particularly from federal agencies like NIH. This initiative coincides with the recent grand opening of the NextGen Precision Health research building, which houses a newly upgraded imaging center with a Krios G4 and Aquilos Cryo-FIB. Other investments in structural biology include a share of ALS beamline 4.2.2 and a Bruker 800 MHz NMR with cryoprobe. For more information, please see: https://provost.missouri.edu/mizzou-forward/ -- Jack Tanner (tannerjj(a)missouri.edu<mailto:[email protected]>) and Lesa Beamer (BeamerL(a)missouri.edu<mailto:[email protected]>) Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211

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