January 2022 - phenixbb - phenix-online.org

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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