- phenixbb - phenix-online.org

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

1 0

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

1 0

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

7 9

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

1 0

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/ > >

4 4

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/ >>> >>>

2 1

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/

3 3

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.

1 0

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

1 0

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 ] --

1 0

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.

1 0

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

2 1

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

2 1

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 > > >

1 0

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

1 1

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

2 1

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

1 0

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

1 0

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

2 1

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

3 3

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

1 0

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.

2 2

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.

1 0

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>

1 0

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

1 0

Low resolution refinement
by Armando Albert 17 Nov '21

17 Nov '21

Dear all, I have got a very promising MR solution at 5A resolution. Can I refine this structure? Any hint would be very much appreciated Armando

3 4

RapiData 2020 applications open
by Smith, Clyde 15 Nov '21

15 Nov '21

Applications are now open for the 2020 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held in sunny California at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 30 - April 4 2020. Course organizers for 2020 are Silvia Russi, Clyde Smith and Jeney Wierman. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. The application deadline is November 10 2019. Successful applicants will be notified shortly thereafter, and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

1 2

Thresholding for N/Q/H errors in phenix.refine?
by Nicholas Gao 15 Nov '21

15 Nov '21

Hi, For the correction of N/Q/H errors in phenix.refine: is this option binary (that is, can it only be turned on or off)? Or can it be adjusted to be on but its stringency adjusted to an arbitrary scale? https://phenix-online.org/documentation/reference/refinement.html#id19 <--suggests its binary, but asking here for thoroughness. Sincerely, Nicholas Gao

2 1

superpose mrc maps (and also mtz files)
by Georg Mlynek 15 Nov '21

15 Nov '21

Dear Scientific community, I got a few .mrc maps from collaborators. Is there a way in phenix to superpose models and corresponding mrc maps. Using superpose maps I get the error:" This file format CCP4 map is not supported as input for this field; only files of type 'Reflections' are allowed. Also the program Structure comparison does not recognize .mrc files. On top there are also a few mtz files I would like to superpose on the .mrc files. Many thanks, br Georg.

3 3

Phenix bug report [[email protected] - Mon Jun 22 19:42:79 2021]
by Robert Munoz 15 Nov '21

15 Nov '21

User name: Robert Munoz E-mail address: robertm(a)lbl.gov Version: 1.18.2-3874 Platform: mac-intel-osx-x86_64 Comments: Trying to refinement using locscale out map Traceback: RuntimeError : cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/cctbx/maptbx/resolution.h(38): CCTBX_ASSERT(sum_all != 0.) failure. Traceback: File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 181, in run return_value = self.target() File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 76, in __call__ result = self.run() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 908, in run self.result = run(args=self.args, validated=True, log=sys.stdout) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 581, in __init__ self.caller(func = self.initialize, prefix="Initialize") File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 619, in caller status = func(prefix=prefix, **kwargs) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 696, in initialize self.inputs = self.process_inputs() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 675, in process_inputs return process_inputs_stage_1(process_inputs_stage_0_object=pis_0, log=self.log) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 403, in process_inputs_stage_1 crystal_symmetry = model.crystal_symmetry()).result.d99 File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/cctbx/maptbx/__init__.py", line 117, in __init__ d_max = self.d_max) Platform info: __FILE__ = /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = May 17 2020 __TIME__ = 22:35:27 __TIMESTAMP__ = Thu Feb 27 10:57:04 2020 __x86_64__ __APPLE_CC__ = 6000 __GNUC__ = 4 __GNUC_MINOR__ = 2 __GNUC_PATCHLEVEL__ = 1 __clang__ __clang_major__ = 11 __clang_minor__ = 0 __clang_patchlevel__ = 0 __clang_version__ = 11.0.0 (clang-1100.0.33.17) __llvm__ __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.17) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 63 __SSE2__ = 1 BOOST_LIB_VERSION = 1_63 PY_VERSION = 2.7.15 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: None os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-17.7.0-x86_64-i386-64bit platform.architecture(): ('64bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 17,179,869,184 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

2 1

Double difference anomalous maps
by Mark Saper 09 Nov '21

09 Nov '21

I tried the "Isomorphous difference map” action and specified a file for input 1 containing F1+, F1– at one wavelength, and the file input 2 containing F2+,F2– at another wavelength. I selected the appropriate Labels for the columns containing the anomalous data. I then specified in "Advanced Options” to use anomalous differences instead of amplitudes. Will this procedure use the following coefficients for the difference Fourier? ( F1(+) – F1(–) ) – ( F2(+) – F2(–) ), alpha(calc) Can someone confirm if this is indeed what is calculated? Many thanks, Mark Saper __________________ Mark A. Saper, Ph.D. Visiting Professor at the Faculty of Medicine Hebrew University of Jerusalem Ein Kerem Jerusalem ISRAEL saper(a)umich.edu mobile +972 52 815-0480‬ Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

2 1

Parameters in "reference_model" during "real space refinement"
by Coudray, Nicolas 08 Nov '21

08 Nov '21

Hi, I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in https://phenix-online.org/documentation/reference/real_space_refine.html): * hydrogens = False * main_chain = True * side_chain = True * fix_outliers = True * strict_rotamer_matching = False * auto_shutoff_for_ncs = False * secondary_structure_only = False It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information? Thanks, Best, Nicolas ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 2

eLBOW crashes Phenix
by Xavier Brazzolotto 03 Nov '21

03 Nov '21

Hi, I am using the latest stable Phenix release (1.19.2-4158) on macOS (v12.0.1) and I do have an odd bug with Phenix eLBOW. The program by it self runs and generates the expected cif files. If I open REEL to check the models, I do see them but as soon as I exit REEL, it crashes the whole Phenix process. Is it a know bug ? I paste the crash report below if this helps. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: python [57745] Path: /Applications/phenix-1.19.2-4158/*/python.app/Contents/MacOS/python Identifier: com.continuum.python Version: ??? Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2021-11-03 18:05:27.1449 +0100 OS Version: macOS 12.0.1 (21A559) Report Version: 12 Bridge OS Version: 6.0 (19P548) Anonymous UUID: 461A1FA5-1FFE-CC49-2057-0C0BB25A7143 Sleep/Wake UUID: 335CBE5C-1D37-4713-B3EA-80B0E830794F Time Awake Since Boot: 300000 seconds Time Since Wake: 13706 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000020 Exception Codes: 0x0000000000000001, 0x0000000000000020 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [57745] VM Region Info: 0x20 is not in any region. Bytes before following region: 4480602080 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 10b109000-10b10a000 [ 4K] r-x/rwx SM=COW .../MacOS/python Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x7ff81e00bc4f objc_release + 31 1 Foundation 0x7ff81f1ecde8 empty + 58 2 Foundation 0x7ff81f094dd9 dealloc + 38 3 Foundation 0x7ff81f094d64 -[NSConcreteMapTable dealloc] + 54 4 libobjc.A.dylib 0x7ff81e0290fe objc_object::sidetable_release(bool, bool) + 232 5 AppKit 0x7ff8212d8c4c ___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2 + 2233 6 AppKit 0x7ff820d3130c NSDisplayCycleObserverInvoke + 155 7 AppKit 0x7ff820d30e97 NSDisplayCycleFlush + 952 8 QuartzCore 0x7ff8252a5434 CA::Transaction::run_commit_handlers(CATransactionPhase) + 98 9 QuartzCore 0x7ff8252a41b2 CA::Transaction::commit() + 376 10 AppKit 0x7ff820dd24e2 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 285 11 AppKit 0x7ff821518724 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 12 CoreFoundation 0x7ff81e23bc07 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 13 CoreFoundation 0x7ff81e23baa4 __CFRunLoopDoObservers + 543 14 CoreFoundation 0x7ff81e23af37 __CFRunLoopRun + 841 15 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 16 HIToolbox 0x7ff826e583e1 RunCurrentEventLoopInMode + 292 17 HIToolbox 0x7ff826e58008 ReceiveNextEventCommon + 284 18 HIToolbox 0x7ff826e57ed5 _BlockUntilNextEventMatchingListInModeWithFilter + 70 19 AppKit 0x7ff820c658f0 _DPSNextEvent + 886 20 AppKit 0x7ff820c63f5c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1411 21 AppKit 0x7ff820c56359 -[NSApplication run] + 586 22 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d2b0a23 wxGUIEventLoop::OSXDoRun() + 115 23 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d192ce4 wxCFEventLoop::DoRun() + 52 24 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d0c2885 wxEventLoopBase::Run() + 165 25 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d087521 wxAppConsoleBase::MainLoop() + 209 26 _core_.so 0x10bd94114 wxPyApp::MainLoop() + 84 27 _core_.so 0x10bdf7902 _wrap_PyApp_MainLoop(_object*, _object*) + 82 28 libpython2.7.dylib 0x10b4967ee PyEval_EvalFrameEx + 30382 29 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 30 libpython2.7.dylib 0x10b409a84 function_call + 388 31 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 32 libpython2.7.dylib 0x10b3ee5d4 instancemethod_call + 180 33 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 34 libpython2.7.dylib 0x10b4957b6 PyEval_EvalFrameEx + 26230 35 libpython2.7.dylib 0x10b49c631 fast_function + 337 36 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 37 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 38 libpython2.7.dylib 0x10b49c54a fast_function + 106 39 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 40 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 41 libpython2.7.dylib 0x10b48e642 PyEval_EvalCode + 34 42 libpython2.7.dylib 0x10b4c0901 PyRun_FileExFlags + 161 43 libpython2.7.dylib 0x10b4c035f PyRun_SimpleFileExFlags + 847 44 libpython2.7.dylib 0x10b4d8dfb Py_Main + 3483 45 dyld 0x11609f4fe start + 462 Thread 1:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff81e138aba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x7ff81e138e2b mach_msg + 59 2 CoreFoundation 0x7ff81e23ca42 __CFRunLoopServiceMachPort + 319 3 CoreFoundation 0x7ff81e23b11b __CFRunLoopRun + 1325 4 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 5 AppKit 0x7ff820dd3cec _NSEventThread + 132 6 libsystem_pthread.dylib 0x7ff81e175514 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff81e17102f thread_start + 15 Thread 2: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 4:: Dispatch queue: com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController 0 CoreFoundation 0x7ff81e1c5746 CFHash + 134 1 CoreFoundation 0x7ff81e1e49fb CFBasicHashAddValue + 223 2 CoreFoundation 0x7ff81e22e09c CFSetCreate + 66 3 CoreFoundation 0x7ff81e223179 CFRunLoopPerformBlock + 288 4 ViewBridge 0x7ff82572020d deferBlockOntoMainThread + 280 5 ViewBridge 0x7ff82572d4d5 deferNSXPCInvocationOntoMainThread + 130 6 Foundation 0x7ff81f0acc12 -[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:] + 1576 7 Foundation 0x7ff81f063f1a message_handler + 206 8 libxpc.dylib 0x7ff81deba530 _xpc_connection_call_event_handler + 56 9 libxpc.dylib 0x7ff81deb928c _xpc_connection_mach_event + 1387 10 libdispatch.dylib 0x7ff81dfbed63 _dispatch_client_callout4 + 9 11 libdispatch.dylib 0x7ff81dfd78b7 _dispatch_mach_msg_invoke + 452 12 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 13 libdispatch.dylib 0x7ff81dfd83fb _dispatch_mach_invoke + 484 14 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 15 libdispatch.dylib 0x7ff81dfc57c8 _dispatch_lane_invoke + 366 16 libdispatch.dylib 0x7ff81dfcf7e1 _dispatch_workloop_worker_thread + 758 17 libsystem_pthread.dylib 0x7ff81e17208f _pthread_wqthread + 326 18 libsystem_pthread.dylib 0x7ff81e17101b start_wqthread + 15 Thread 5: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 10: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 11: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 12: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x6000000000000000 rbx: 0x0000000000000018 rcx: 0x0000000000000000 rdx: 0x00007f8ec5973a00 rdi: 0x00007f8ea57830d0 rsi: 0x0000000000000000 rbp: 0x00007ff7b4df3260 rsp: 0x00007ff7b4df3238 r8: 0x0000000000000200 r9: 0x00007f8ec5972d20 r10: 0x00007ff85f8105d0 r11: 0x00007ff81f094d2e r12: 0x00007f8f01f8e7c0 r13: 0x00007ff85f966a01 r14: 0x00007f8f01f8e7c8 r15: 0x000000000000000d rip: 0x00007ff81e00bc4f rfl: 0x0000000000010246 cr2: 0x0000000000000020 Logical CPU: 0 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Thread 0 instruction stream: 34 48 89 c2 48 01 ca 72-12 f0 48 0f b1 17 74 25 4H..H..r..H...t% a8 01 75 e4 31 f6 e9 7c-d7 01 00 31 f6 e9 eb 86 ..u.1..|...1.... 00 00 48 b9 f8 ff ff ff-ff 7f 00 00 48 21 c8 f6 ..H.........H!.. 40 1c 01 74 df 48 89 f8-c3 90 90 90 90 90 90 90 @..t.H.......... 90 48 85 ff 74 76 89 f8-83 e0 01 48 85 c0 75 6c .H..tv.....H..ul 48 8b 07 48 b9 f8 ff ff-ff ff 7f 00 00 48 21 c1 H..H.........H!. [48]8b 51 20 f6 c2 04 74-54 a8 01 74 6f 48 b9 00 H.Q ...tT..toH.. <== 00 00 00 00 00 80 00 48-ba 00 00 00 00 00 00 00 .......H........ 01 48 39 c8 72 36 48 89-c6 48 29 d6 72 17 f0 48 .H9.r6H..H).r..H 0f b1 37 74 22 a8 01 75-e8 31 f6 ba 01 00 00 00 ..7t"..u.1...... e9 82 d3 01 00 48 85 c8-75 3a 48 8b 35 18 f5 99 .....H..u:H.5... 41 ff 25 f2 d2 e6 3f 48-39 ce 72 ee c3 f6 c2 02 A.%...?H9.r..... Binary Images: 0x7ff81e003000 - 0x7ff81e03cfff libobjc.A.dylib (*) <7cfcdc89-2bee-3784-b7af-c676f60fe211> /usr/lib/libobjc.A.dylib 0x7ff81f042000 - 0x7ff81f3fcfff com.apple.Foundation (6.9) <d7fd0214-4bbb-3d84-88f7-820b25a6e16c> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation 0x7ff820c27000 - 0x7ff821ab3fff com.apple.AppKit (6.9) <dd0028a3-78e3-3a8a-a51b-ddd68123adef> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x7ff8252a2000 - 0x7ff825589fff com.apple.QuartzCore (1.11) <7e85dee1-5bb8-3ac2-ad98-2552838e01ca> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore 0x7ff81e1bc000 - 0x7ff81e6befff com.apple.CoreFoundation (6.9) <3002b545-6841-3fc8-91a2-bcfbe5872465> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x7ff826e29000 - 0x7ff827120fff com.apple.HIToolbox (2.1.1) <4163a93f-bf71-3219-80ed-6f65e9266b81> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox 0x10d07d000 - 0x10dd33fff libwx_osx_cocoau-3.0.0.2.0.dylib (*) <72694e85-a8dd-368c-b1ab-3157eceee77a> /Applications/phenix-1.19.2-4158/*/libwx_osx_cocoau-3.0.0.2.0.dylib 0x10bd93000 - 0x10bec9fff _core_.so (*) <58a38f93-fa30-3ff4-9c13-36bb95f0c81e> /Applications/phenix-1.19.2-4158/*/_core_.so 0x10b3cd000 - 0x10b51dfff libpython2.7.dylib (*) <92f45f91-3cd1-3a32-9811-5b8e3c7e2fc3> /Applications/phenix-1.19.2-4158/*/libpython2.7.dylib 0x11609a000 - 0x116105fff dyld (*) <1a6ae033-9438-33c0-8077-988fd885250a> /usr/lib/dyld 0x7ff81e138000 - 0x7ff81e16efff libsystem_kernel.dylib (*) <12bd6f13-c452-35ee-9069-51befef29f1a> /usr/lib/system/libsystem_kernel.dylib 0x7ff81e16f000 - 0x7ff81e17afff libsystem_pthread.dylib (*) <29a2750e-f31b-3630-8761-242a6bc3e99e> /usr/lib/system/libsystem_pthread.dylib 0x7ff82571a000 - 0x7ff82580dfff com.apple.ViewBridge (637.9) <ff66b120-2752-3809-87d8-9c95c0bb2988> /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge 0x7ff81dead000 - 0x7ff81dee3fff libxpc.dylib (*) <900e1f8b-6333-3e4d-b64c-751264bb7223> /usr/lib/system/libxpc.dylib 0x7ff81dfbc000 - 0x7ff81e002fff libdispatch.dylib (*) <be53a13c-8ce1-3e40-b9bc-98473d3eed3e> /usr/lib/system/libdispatch.dylib 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%) Writable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 896K 7 Activity Tracing 256K 1 CG backing stores 2528K 4 CG image 1596K 41 CG raster data 184K 21 ColorSync 228K 26 CoreAnimation 139.5M 206 CoreGraphics 12K 2 CoreImage 608K 35 CoreUI image data 2480K 21 Foundation 80K 2 Kernel Alloc Once 8K 1 MALLOC 511.7M 149 MALLOC guard page 48K 9 MALLOC_MEDIUM (reserved) 880.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 13 Stack 14.1M 13 VM_ALLOCATE 1128K 27 VM_ALLOCATE (reserved) 768.0M 1 reserved VM address space (unallocated) __DATA 41.4M 510 __DATA_CONST 23.2M 234 __DATA_DIRTY 969K 139 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 682.2M 110 __OBJC_RO 81.5M 1 __OBJC_RW 3120K 2 __TEXT 529.9M 498 __UNICODE 588K 1 dyld private memory 3072K 3 mapped file 158.3M 26 shared memory 1296K 19 =========== ======= ======= TOTAL 4.2G 2133 TOTAL, minus reserved VM space 2.2G 2133 ----------- Full Report ----------- {"app_name":"python","timestamp":"2021-11-03 18:05:27.00 +0100","app_version":"","slice_uuid":"41b01d14-4c6e-3a14-a84e-812c0ee8d9cd","build_version":"","platform":1,"bundleID":"com.continuum.python","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"3B71C390-9A85-4125-A53A-7058CF9E1361","name":"python"} { "uptime" : 300000, "procLaunch" : "2021-11-03 18:04:29.4653 +0100", "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro15,1", "procStartAbsTime" : 303473294854732, "coalitionID" : 1512, "osVersion" : { "train" : "macOS 12.0.1", "build" : "21A559", "releaseType" : "User" }, "captureTime" : "2021-11-03 18:05:27.1449 +0100", "incident" : "3B71C390-9A85-4125-A53A-7058CF9E1361", "bug_type" : "309", "pid" : 57745, "procExitAbsTime" : 303530973462636, "cpuType" : "X86-64", "procName" : "python", "procPath" : "\/Applications\/phenix-1.19.2-4158\/*\/python.app\/Contents\/MacOS\/python", "bundleInfo" : {"CFBundleIdentifier":"com.continuum.python"}, "storeInfo" : {"deviceIdentifierForVendor":"4FD8A66E-22D2-5A3D-904B-4E69B0B05DAE","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "org.pythonmac.unspecified.phenix-1.19.2-4158", "crashReporterKey" : "461A1FA5-1FFE-CC49-2057-0C0BB25A7143", "responsiblePid" : 57744, "wakeTime" : 13706, "bridgeVersion" : {"build":"19P548","train":"6.0"}, "sleepWakeUUID" : "335CBE5C-1D37-4713-B3EA-80B0E830794F", "sip" : "enabled", "vmRegionInfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python", "isCorpse" : 1, "exception" : {"codes":"0x0000000000000001, 0x0000000000000020","rawCodes":[1,32],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000020"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":57745}, "vmregioninfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python", "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 0, "threads" : [{"triggered":true,"id":3110783,"instructionState":{"instructionStream":{"bytes":[52,72,137,194,72,1,202,114,18,240,72,15,177,23,116,37,168,1,117,228,49,246,233,124,215,1,0,49,246,233,235,134,0,0,72,185,248,255,255,255,255,127,0,0,72,33,200,246,64,28,1,116,223,72,137,248,195,144,144,144,144,144,144,144,144,72,133,255,116,118,137,248,131,224,1,72,133,192,117,108,72,139,7,72,185,248,255,255,255,255,127,0,0,72,33,193,72,139,81,32,246,194,4,116,84,168,1,116,111,72,185,0,0,0,0,0,0,128,0,72,186,0,0,0,0,0,0,0,1,72,57,200,114,54,72,137,198,72,41,214,114,23,240,72,15,177,55,116,34,168,1,117,232,49,246,186,1,0,0,0,233,130,211,1,0,72,133,200,117,58,72,139,53,24,245,153,65,255,37,242,210,230,63,72,57,206,114,238,195,246,194,2],"offset":96}},"threadState":{"r13":{"value":140704732310017,"symbolLocation":33,"symbol":"loadImageFuncs"},"rax":{"value":6917529027641081856},"rflags":{"value":66118},"cpu":{"value":0},"r14":{"value":140252190140360},"rsi":{"value":0},"r8":{"value":512},"cr2":{"value":32},"rdx":{"value":140251177105920},"r10":{"value":140704730908112,"symbolLocation":0,"symbol":"OBJC_CLASS_$_NSConcreteMapTable"},"r9":{"value":140251177102624},"r15":{"value":13},"rbx":{"value":24},"trap":{"value":14,"description":"(no mapping for user data read)"},"err":{"value":4},"r11":{"value":140703649320238,"symbolLocation":0,"symbol":"-[NSConcreteMapTable dealloc]"},"rip":{"value":140703631981647,"matchesCrashFrame":1},"rbp":{"value":140701868175968},"rsp":{"value":140701868175928},"r12":{"value":140252190140352},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":140250638201040}},"queue":"com.apple.main-thread","frames":[{"imageOffset":35919,"symbol":"objc_release","symbolLocation":31,"imageIndex":0},{"imageOffset":1748456,"symbol":"empty","symbolLocation":58,"imageIndex":1},{"imageOffset":339417,"symbol":"dealloc","symbolLocation":38,"imageIndex":1},{"imageOffset":339300,"symbol":"-[NSConcreteMapTable dealloc]","symbolLocation":54,"imageIndex":1},{"imageOffset":155902,"symbol":"objc_object::sidetable_release(bool, bool)","symbolLocation":232,"imageIndex":0},{"imageOffset":7019596,"symbol":"___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2","symbolLocation":2233,"imageIndex":2},{"imageOffset":1090316,"symbol":"NSDisplayCycleObserverInvoke","symbolLocation":155,"imageIndex":2},{"imageOffset":1089175,"symbol":"NSDisplayCycleFlush","symbolLocation":952,"imageIndex":2},{"imageOffset":13364,"symbol":"CA::Transaction::run_commit_handlers(CATransactionPhase)","symbolLocation":98,"imageIndex":3},{"imageOffset":8626,"symbol":"CA::Transaction::commit()","symbolLocation":376,"imageIndex":3},{"imageOffset":1750242,"symbol":"__62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke","symbolLocation":285,"imageIndex":2},{"imageOffset":9377572,"symbol":"___NSRunLoopObserverCreateWithHandler_block_invoke","symbolLocation":41,"imageIndex":2},{"imageOffset":523271,"symbol":"__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__","symbolLocation":23,"imageIndex":4},{"imageOffset":522916,"symbol":"__CFRunLoopDoObservers","symbolLocation":543,"imageIndex":4},{"imageOffset":519991,"symbol":"__CFRunLoopRun","symbolLocation":841,"imageIndex":4},{"imageOffset":517421,"symbol":"CFRunLoopRunSpecific","symbolLocation":563,"imageIndex":4},{"imageOffset":193505,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":5},{"imageOffset":192520,"symbol":"ReceiveNextEventCommon","symbolLocation":284,"imageIndex":5},{"imageOffset":192213,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":70,"imageIndex":5},{"imageOffset":256240,"symbol":"_DPSNextEvent","symbolLocation":886,"imageIndex":2},{"imageOffset":249692,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1411,"imageIndex":2},{"imageOffset":193369,"symbol":"-[NSApplication run]","symbolLocation":586,"imageIndex":2},{"imageOffset":2308643,"symbol":"wxGUIEventLoop::OSXDoRun()","symbolLocation":115,"imageIndex":6},{"imageOffset":1137892,"symbol":"wxCFEventLoop::DoRun()","symbolLocation":52,"imageIndex":6},{"imageOffset":284805,"symbol":"wxEventLoopBase::Run()","symbolLocation":165,"imageIndex":6},{"imageOffset":42273,"symbol":"wxAppConsoleBase::MainLoop()","symbolLocation":209,"imageIndex":6},{"imageOffset":4372,"symbol":"wxPyApp::MainLoop()","symbolLocation":84,"imageIndex":7},{"imageOffset":411906,"symbol":"_wrap_PyApp_MainLoop(_object*, _object*)","symbolLocation":82,"imageIndex":7},{"imageOffset":825326,"symbol":"PyEval_EvalFrameEx","symbolLocation":30382,"imageIndex":8},{"imageOffset":794291,"symbol":"PyEval_EvalCodeEx","symbolLocation":2147,"imageIndex":8},{"imageOffset":248452,"symbol":"function_call","symbolLocation":388,"imageIndex":8},{"imageOffset":64737,"symbol":"PyObject_Call","symbolLocation":97,"imageIndex":8},{"imageOffset":136660,"symbol":"instancemethod_call","symbolLocation":180,"imageIndex":8},{"imageOffset":64737,"symbol":"PyObject_Call","symbolLocation":97,"imageIndex":8},{"imageOffset":821174,"symbol":"PyEval_EvalFrameEx","symbolLocation":26230,"imageIndex":8},{"imageOffset":849457,"symbol":"fast_function","symbolLocation":337,"imageIndex":8},{"imageOffset":821385,"symbol":"PyEval_EvalFrameEx","symbolLocation":26441,"imageIndex":8},{"imageOffset":794291,"symbol":"PyEval_EvalCodeEx","symbolLocation":2147,"imageIndex":8},{"imageOffset":849226,"symbol":"fast_function","symbolLocation":106,"imageIndex":8},{"imageOffset":821385,"symbol":"PyEval_EvalFrameEx","symbolLocation":26441,"imageIndex":8},{"imageOffset":794291,"symbol":"PyEval_EvalCodeEx","symbolLocation":2147,"imageIndex":8},{"imageOffset":792130,"symbol":"PyEval_EvalCode","symbolLocation":34,"imageIndex":8},{"imageOffset":997633,"symbol":"PyRun_FileExFlags","symbolLocation":161,"imageIndex":8},{"imageOffset":996191,"symbol":"PyRun_SimpleFileExFlags","symbolLocation":847,"imageIndex":8},{"imageOffset":1097211,"symbol":"Py_Main","symbolLocation":3483,"imageIndex":8},{"imageOffset":21758,"symbol":"start","symbolLocation":462,"imageIndex":9}]},{"id":3110821,"name":"com.apple.NSEventThread","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":10},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":10},{"imageOffset":526914,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":4},{"imageOffset":520475,"symbol":"__CFRunLoopRun","symbolLocation":1325,"imageIndex":4},{"imageOffset":517421,"symbol":"CFRunLoopRunSpecific","symbolLocation":563,"imageIndex":4},{"imageOffset":1756396,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":2},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":11},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":11}]},{"id":3111061,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111064,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111066,"queue":"com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController","frames":[{"imageOffset":38726,"symbol":"CFHash","symbolLocation":134,"imageIndex":4},{"imageOffset":166395,"symbol":"CFBasicHashAddValue","symbolLocation":223,"imageIndex":4},{"imageOffset":467100,"symbol":"CFSetCreate","symbolLocation":66,"imageIndex":4},{"imageOffset":422265,"symbol":"CFRunLoopPerformBlock","symbolLocation":288,"imageIndex":4},{"imageOffset":25101,"symbol":"deferBlockOntoMainThread","symbolLocation":280,"imageIndex":12},{"imageOffset":79061,"symbol":"deferNSXPCInvocationOntoMainThread","symbolLocation":130,"imageIndex":12},{"imageOffset":437266,"symbol":"-[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:]","symbolLocation":1576,"imageIndex":1},{"imageOffset":139034,"symbol":"message_handler","symbolLocation":206,"imageIndex":1},{"imageOffset":54576,"symbol":"_xpc_connection_call_event_handler","symbolLocation":56,"imageIndex":13},{"imageOffset":49804,"symbol":"_xpc_connection_mach_event","symbolLocation":1387,"imageIndex":13},{"imageOffset":11619,"symbol":"_dispatch_client_callout4","symbolLocation":9,"imageIndex":14},{"imageOffset":112823,"symbol":"_dispatch_mach_msg_invoke","symbolLocation":452,"imageIndex":14},{"imageOffset":35717,"symbol":"_dispatch_lane_serial_drain","symbolLocation":335,"imageIndex":14},{"imageOffset":115707,"symbol":"_dispatch_mach_invoke","symbolLocation":484,"imageIndex":14},{"imageOffset":35717,"symbol":"_dispatch_lane_serial_drain","symbolLocation":335,"imageIndex":14},{"imageOffset":38856,"symbol":"_dispatch_lane_invoke","symbolLocation":366,"imageIndex":14},{"imageOffset":79841,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":758,"imageIndex":14},{"imageOffset":12431,"symbol":"_pthread_wqthread","symbolLocation":326,"imageIndex":11},{"imageOffset":8219,"symbol":"start_wqthread","symbolLocation":15,"imageIndex":11}]},{"id":3111067,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111068,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111128,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111129,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111130,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111131,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111132,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]},{"id":3111133,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":11}]}], "usedImages" : [ { "source" : "P", "arch" : "x86_64h", "base" : 140703631945728, "size" : 237568, "uuid" : "7cfcdc89-2bee-3784-b7af-c676f60fe211", "path" : "\/usr\/lib\/libobjc.A.dylib", "name" : "libobjc.A.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 140703648980992, "CFBundleShortVersionString" : "6.9", "CFBundleIdentifier" : "com.apple.Foundation", "size" : 3911680, "uuid" : "d7fd0214-4bbb-3d84-88f7-820b25a6e16c", "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation", "name" : "Foundation", "CFBundleVersion" : "1855.105" }, { "source" : "P", "arch" : "x86_64", "base" : 140703678230528, "CFBundleShortVersionString" : "6.9", "CFBundleIdentifier" : "com.apple.AppKit", "size" : 15257600, "uuid" : "dd0028a3-78e3-3a8a-a51b-ddd68123adef", "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit", "name" : "AppKit", "CFBundleVersion" : "2113" }, { "source" : "P", "arch" : "x86_64", "base" : 140703752134656, "CFBundleShortVersionString" : "1.11", "CFBundleIdentifier" : "com.apple.QuartzCore", "size" : 3047424, "uuid" : "7e85dee1-5bb8-3ac2-ad98-2552838e01ca", "path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore", "name" : "QuartzCore", "CFBundleVersion" : "962.57.1" }, { "source" : "P", "arch" : "x86_64h", "base" : 140703633752064, "CFBundleShortVersionString" : "6.9", "CFBundleIdentifier" : "com.apple.CoreFoundation", "size" : 5255168, "uuid" : "3002b545-6841-3fc8-91a2-bcfbe5872465", "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation", "name" : "CoreFoundation", "CFBundleVersion" : "1855.105" }, { "source" : "P", "arch" : "x86_64", "base" : 140703780999168, "CFBundleShortVersionString" : "2.1.1", "CFBundleIdentifier" : "com.apple.HIToolbox", "size" : 3112960, "uuid" : "4163a93f-bf71-3219-80ed-6f65e9266b81", "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox", "name" : "HIToolbox" }, { "source" : "P", "arch" : "x86_64", "base" : 4513583104, "size" : 13332480, "uuid" : "72694e85-a8dd-368c-b1ab-3157eceee77a", "path" : "\/Applications\/phenix-1.19.2-4158\/*\/libwx_osx_cocoau-3.0.0.2.0.dylib", "name" : "libwx_osx_cocoau-3.0.0.2.0.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 4493750272, "size" : 1273856, "uuid" : "58a38f93-fa30-3ff4-9c13-36bb95f0c81e", "path" : "\/Applications\/phenix-1.19.2-4158\/*\/_core_.so", "name" : "_core_.so" }, { "source" : "P", "arch" : "x86_64", "base" : 4483502080, "size" : 1380352, "uuid" : "92f45f91-3cd1-3a32-9811-5b8e3c7e2fc3", "path" : "\/Applications\/phenix-1.19.2-4158\/*\/libpython2.7.dylib", "name" : "libpython2.7.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 4664696832, "size" : 442368, "uuid" : "1a6ae033-9438-33c0-8077-988fd885250a", "path" : "\/usr\/lib\/dyld", "name" : "dyld" }, { "source" : "P", "arch" : "x86_64", "base" : 140703633211392, "size" : 225280, "uuid" : "12bd6f13-c452-35ee-9069-51befef29f1a", "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib", "name" : "libsystem_kernel.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 140703633436672, "size" : 49152, "uuid" : "29a2750e-f31b-3630-8761-242a6bc3e99e", "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib", "name" : "libsystem_pthread.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 140703756820480, "CFBundleShortVersionString" : "637.9", "CFBundleIdentifier" : "com.apple.ViewBridge", "size" : 999424, "uuid" : "ff66b120-2752-3809-87d8-9c95c0bb2988", "path" : "\/System\/Library\/PrivateFrameworks\/ViewBridge.framework\/Versions\/A\/ViewBridge", "name" : "ViewBridge", "CFBundleVersion" : "637.9" }, { "source" : "P", "arch" : "x86_64", "base" : 140703630544896, "size" : 225280, "uuid" : "900e1f8b-6333-3e4d-b64c-751264bb7223", "path" : "\/usr\/lib\/system\/libxpc.dylib", "name" : "libxpc.dylib" }, { "source" : "P", "arch" : "x86_64", "base" : 140703631654912, "size" : 290816, "uuid" : "be53a13c-8ce1-3e40-b9bc-98473d3eed3e", "path" : "\/usr\/lib\/system\/libdispatch.dylib", "name" : "libdispatch.dylib" }, { "size" : 0, "source" : "A", "base" : 0, "uuid" : "00000000-0000-0000-0000-000000000000" } ], "sharedCache" : { "base" : 140703630209024, "size" : 15213641728, "uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01" }, "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 896K 7 \nActivity Tracing 256K 1 \nCG backing stores 2528K 4 \nCG image 1596K 41 \nCG raster data 184K 21 \nColorSync 228K 26 \nCoreAnimation 139.5M 206 \nCoreGraphics 12K 2 \nCoreImage 608K 35 \nCoreUI image data 2480K 21 \nFoundation 80K 2 \nKernel Alloc Once 8K 1 \nMALLOC 511.7M 149 \nMALLOC guard page 48K 9 \nMALLOC_MEDIUM (reserved) 880.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nSTACK GUARD 56.0M 13 \nStack 14.1M 13 \nVM_ALLOCATE 1128K 27 \nVM_ALLOCATE (reserved) 768.0M 1 reserved VM address space (unallocated)\n__DATA 41.4M 510 \n__DATA_CONST 23.2M 234 \n__DATA_DIRTY 969K 139 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 682.2M 110 \n__OBJC_RO 81.5M 1 \n__OBJC_RW 3120K 2 \n__TEXT 529.9M 498 \n__UNICODE 588K 1 \ndyld private memory 3072K 3 \nmapped file 158.3M 26 \nshared memory 1296K 19 \n=========== ======= ======= \nTOTAL 4.2G 2133 \nTOTAL, minus reserved VM space 2.2G 2133 \n", "legacyInfo" : { "threadTriggered" : { "queue" : "com.apple.main-thread" } }, "trialInfo" : { "rollouts" : [ { "rolloutId" : "602ad4dac86151000cf27e46", "factorPackIds" : { "SIRI_DICTATION_ASSETS" : "6169fcad436117010456880e" }, "deploymentId" : 240000238 }, { "rolloutId" : "60da5e84ab0ca017dace9abf", "factorPackIds" : { }, "deploymentId" : 240000008 }, { "rolloutId" : "607844aa04477260f58a8077", "factorPackIds" : { "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a" }, "deploymentId" : 240000066 }, { "rolloutId" : "5fc94383418129005b4e9ae0", "factorPackIds" : { }, "deploymentId" : 240000153 }, { "rolloutId" : "5ffde50ce2aacd000d47a95f", "factorPackIds" : { }, "deploymentId" : 240000068 }, { "rolloutId" : "601d9415f79519000ccd4b69", "factorPackIds" : { "SIRI_TEXT_TO_SPEECH" : "618057de778e4b2a1cf6a5d5" }, "deploymentId" : 240000299 } ], "experiments" : [ ] } } Model: MacBookPro15,1, BootROM 1715.40.15.0.0 (iBridge: 19.16.10548.0.0,0), 6 processors, 6-Core Intel Core i9, 2,9 GHz, 32 GB, SMC Graphics: Intel UHD Graphics 630, Intel UHD Graphics 630, Built-In Graphics: Radeon Pro 560X, Radeon Pro 560X, PCIe, 4 GB Display: Color LCD, 2880 x 1800 Retina, Main, MirrorOff, Online Memory Module: BANK 0/ChannelA-DIMM0, 16 GB, DDR4, 2400 MHz, Micron, 16ATS2G64HZ-2G6B1 Memory Module: BANK 2/ChannelB-DIMM0, 16 GB, DDR4, 2400 MHz, Micron, 16ATS2G64HZ-2G6B1 AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x7BF), wl0: Jul 12 2021 19:26:30 version 9.30.464.0.32.5.76 FWID 01-45ccefcd Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: T2Bus USB Device: Touch Bar Backlight USB Device: Touch Bar Display USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 47.5 Thunderbolt Bus: MacBook Pro, Apple Inc., 47.5

1 0

Phenix 1.20 release candidates
by Billy Poon 02 Nov '21

02 Nov '21

Hi everyone, We are doing a final Python 2.7 release of Phenix and the first release candidate is available from https://phenix-online.org/download/nightly_builds.cgi This release will contain several new features, such as tools for using AlphaFold models. The release after that is planned to be in Python 3.7. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

1 2

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 27 Oct '21

27 Oct '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 DEC 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template is attached to this email. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

1 0

Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 19 Oct '21

19 Oct '21

Thanks for that suggestion, Phil. After several weeks, I've finally found solid answers to all my questions, which I'll write here in case anyone reading this message is curious: Q1: Is there any way to apply different map weights to different pieces of the structure during refinement? A1: Pavel tells me the answer is no—this feature is not available in Phenix yet. The way I was able to accomplish something to a similar effect was by performing full-model refinements at different weights. Then, in a final refinement job, use torsion restraints from each of those output models (as reference models) across the desired stretches of residues. Clunky, but it solved a few problems for me. Q2: How is the generic "weight" parameter at the bottom of the Phenix GUI applied to the refinement? A2: The target function is T = Tmap * weight + Trestraints. At the time of writing this message, there is a typo in the Phenix Real-Space Refine documentation, which incorrectly reports the target function as "T = Tmap + weight * Trestraints" (Pavel confirmed). Q3: Why is the PDB validation telling me I have geometric issues that were not acknowledged by Phenix? A3: Phil is right. The ESD for several nucleic acid bond lengths and angles is wide as compared to the sigma tolerated by wwPDB. To fix this, I went into the CIF files within the geostd folder and made the following changes to the troublesome RNA and DNA nucleotide files: *data_AD.cif, data_TD.cif, data_CD.cif, data_GD.cif:* length: C1'-N1, ESD=0.020 C3'-O3', ESD=0.020 angles: O4'-C1'-N9/N1, ESD=0.30 *data_U.cif* angles: C5-C6-N1, ESD=0.5 C6-N1-C2, ESD=0.5 *data_C.cif* angles: C6-N1-C2, ESD=0.5 *data_A.cif* angles: N7-C8-N9, ESD=0.5 Best, Josh On Mon, Sep 13, 2021 at 7:23 AM Philip D. Jeffrey <pjeffrey(a)princeton.edu> wrote: > :: most of the outliers are not acknowledged as such (by Phenix), and I > only become > :: aware of them when the wwPDB validation tells me they are there. > > Check that the equilibrium values that PDB are using and the ones that > Phenix are using are the same. If they're not (or if the sigmas are way > different) you're not going to be able to change the outcome just by > changing weights. > > Phil Jeffrey > Princeton > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org < > phenixbb-bounces(a)phenix-online.org> on behalf of Josh Cofsky < > josh.cofsky(a)gmail.com> > *Sent:* Sunday, September 12, 2021 9:42 PM > *To:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] Restricting real-space refinement and weights > to specific atom selections > > I now realize that I am confused as to what the mentioned "weight" > parameter refers to. The Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should yield greater conformity to > geometric restraints at the expense of model/map fit. In reality, I observe > the opposite trend in my refinements (which is why I assumed it was a "map > weight"). Can someone clarify what "weight" (Refinement Settings > "Other > Options") refers to? > > The reason I am exploring these questions is that Phenix RSR is > introducing bond angle outliers into a low-resolution area of a DNA > molecule in my model—most of the outliers are not acknowledged as such (by > Phenix), and I only become aware of them when the wwPDB validation tells me > they are there. I assumed this was the result of overfitting to the map > because setting "weight" to 0.0 prevented these outliers from appearing, > but at the expense of map-model fit in the remainder of the structure > (which is why I wanted to apply different weights to different segments of > the model). > > Thanks, > Josh > > On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky(a)gmail.com> > wrote: > > Hi all, > > I'm using phenix.real_space_refine to refine a model into a cryo-EM map. > My local map resolution is highly variable across the molecule, and using a > single map weight (the parameter shown in the Refinement Settings > "Other > Options" in the GUI) on the whole model leads to poor map-to-model fit in > some locations and overfitting in others. Potential solutions could be to: > 1. assign different map weights to different segments of the model (based > on a user-specified atom selection) > OR > 2. perform iterative refinements with different weight settings, holding > different (user-specified) segments of the model fixed during each > iteration (I suspect this isn't possible based on Pavel's message here: > http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) > > Is either of these approaches (or another one that accomplishes the same > goal) possible? I am using the Phenix GUI, but if this is only possible in > command line, and you're willing to share an example command that > accomplishes either of these tasks, please let me know. > > Thanks! > -Josh > > (also, apologies if this is a duplicate message...still trying to figure > out the phenixbb listserv) > >

1 0

Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 15 Oct '21

15 Oct '21

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

1 0

missing statistics for rama-z
by Hannah Bridges 15 Oct '21

15 Oct '21

Hello, I have a PDB for which, when I run either realspace refinement or validation, phenix does not show rama-z scores for helix or sheet (and the structure is not entirely loops..) Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.08), residues: 8101 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.06), residues: 8101 It seems peculiar to this one model, as other very similar ones are fine, but is this something that other people have seen before? I can supply the PBD off-list for investigation. Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

3 3

Nightly build downloads
by Armando Albert 01 Oct '21

01 Oct '21

Dear all, I am unable to find the nightly build releases from the Phenix web page. Is there any issue I do not know? Armando

4 3

Phenix website change complete
by Dorothee Liebschner 30 Sep '21

30 Sep '21

Hi everyone, We changed the website. Let us know if there are any issues. Best wishes, The Phenix Team -- 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

1 0

Phenix website maintenance on 9/30/2021
by Dorothee Liebschner 29 Sep '21

29 Sep '21

Hi everyone, The Phenix website will be changed tomorrow, Thursday 9/30/2021. Therefore, the website might not be available for a couple of hours. If you encounter any problems after the switch - which we will announce on the BB - please let us know. We will change the urls of some pages due to some reorganization, but the addresses of the most visited pages should be the same, such as download, documentation and so on. Best wishes, The Phenix Team -- 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

1 0

problems with phenix.refine and wwPDB deposition
by Błażej Bagiński 24 Sep '21

24 Sep '21

Dear fellow Phenix bulletin boarders, I'd like to ask for help with refinement-deposition file conflict. I 'finished' solving the structure (protein, 1 chain, 2 ligands), doing the final refinement in phenix.refine. Structure looks okay and does not report any errors in phenix/coot. I than started the deposition with the wwPDB OneDep System.After long check, my files were rejected (multiple errors, with the best one being "coordinates not found"). Following the FAQ, I run the prepare_pdb_deposition, but the results were the same. I also tried using PDB_Extract (https://pdb-extract.wwpdb.org/), with its result file also generating plethora of errors. As a control, I put the same phenix.refine file into the PDB-REDO server, and its results finished wwPDB validation successfully. Trouble is, PDB-REDO is quite aggressive and messed up one ligand, occupancies and two loops, so I would prefer to not submit it for anyone to see. How do you make refinement output compatible with wwPDB? Is there a way to run PDB-REDO without the REDO? Kind regards, Blazej Baginski

3 2

Download issues
by Billy Poon 24 Sep '21

24 Sep '21

Hi everyone, If you are having download issues, can you post a message here? We are seeing reports of download issues from some users and we want to determine how widespread the issue is. Some users have said that the download works after waiting for a bit or by using the incognito or private mode of their browser. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

1 1

Postdoctoral Research Opportunity in Cryo-EM at University of Washington, in Seattle, USA
by George Wisedchaisri 18 Sep '21

18 Sep '21

Hi, I have a job opening announcement for a joint postdoctoral position in the Catterall and Zheng Labs at University of Washington, in Seattle, WA, USA. Please see the link below for more detailed info. http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20210913/9614f6ba/att… Thanks, George Wisedchaisri -- *Postdoctoral Research Position* *Senior Fellow or Instructor Appointment Level* *Structural Basis for Function and Pharmacology of Voltage Gated Sodium and Calcium Channels* *Laboratories of William A. Catterall and Ning Zheng* *Department of Pharmacology, University of Washington, Seattle, WA 98195-7280 USA* *Please respond by e-mail to wcattlab(a)uw.edu <wcattlab(a)uw.edu> with Postdoctoral Application on the Subject Line* *Position Requirements* PhD or equivalent in biochemistry, biophysics, bioengineering, or structural biology. Experience in molecular biology, cell culture, and protein expression, purification, and characterization. Excellent communication skills and successful experience in a team research environment. Two years experience with cryo-EM data collection, processing, and analysis. Successful determination of a protein structure by cryo-EM. *Application Requirements* Curriculum Vitae Names of three referees *University of Washington is an affirmative action, equal opportunity employer. All qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, national origin, age, protected veteran or disabled status, or genetic information.* -- George Wisedchaisri, Ph.D. Research Assistant Professor of Pharmacology --------------------------------------------- University of Washington School of Medicine Department of Pharmacology 1959 NE Pacific St Seattle, WA 98195-7280

1 0

Today is the last day to register for the SSRL/LCLS User Meeting
by Mooers, Blaine H.M. (HSC) 17 Sep '21

17 Sep '21

Dear Phenixbb: Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free and virtual. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster session is like playing a 1990s computer game. I was on the poster judging team. We spent this week judging the posters virtually. We made our selections of the seven poster prize finalists today. All of the semifinalist posters were excellent. Best regards, Blaine SSRL UEC member and past chair. 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

1 0

(no subject)
by Smita Yadav 17 Sep '21

17 Sep '21

Dear All, hello to everyone. I wanted to know which gromac version is mostly used for simulation in linux. -- With Regards Smita Yadav

2 1

NIH-funded Postdoc, Membrane Protein Structural Biology (Nebraska, USA)
by Alex Vecchio 14 Sep '21

14 Sep '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 recent or soon-to-be Ph.D., with experience in membrane proteins and one structural technique. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via a recently well-scored NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-postdoc…> . 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

1 0

Assistant Researcher Senior Position in the KU Protein Structure Laboratory
by Lovell, Scott W 13 Sep '21

13 Sep '21

The Protein Structure and X-ray Crystallography Laboratory (PSXL) at the University of Kansas (KU) is seeking a full-time Assistant Researcher Senior to work on a variety of structural biology projects. As a core laboratory, the PSXL collaborates with multiple investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSXL is involved in NIAID funded R01 grants and manages the structural biology efforts for projects aimed at antiviral inhibitor development. As such, this position will involve structural biology work to facilitate the structure-guided development of inhibitors targeting the MERS-CoV and SARS-CoV-2 main proteases. For a full description of the position and to apply, GO TO: https://employment.ku.edu/staff/20030BR Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 https://psxl.ku.edu/ __________________________________________________

1 0

Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 12 Sep '21

12 Sep '21

Hi all, I'm using phenix.real_space_refine to refine a model into a cryo-EM map. My local map resolution is highly variable across the molecule, and using a single map weight (the parameter shown in the Refinement Settings > "Other Options" in the GUI) on the whole model leads to poor map-to-model fit in some locations and overfitting in others. Potential solutions could be to: 1. assign different map weights to different segments of the model (based on a user-specified atom selection) OR 2. perform iterative refinements with different weight settings, holding different (user-specified) segments of the model fixed during each iteration (I suspect this isn't possible based on Pavel's message here: http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) Is either of these approaches (or another one that accomplishes the same goal) possible? I am using the Phenix GUI, but if this is only possible in command line, and you're willing to share an example command that accomplishes either of these tasks, please let me know. Thanks! -Josh (also, apologies if this is a duplicate message...still trying to figure out the phenixbb listserv)

1 1

Extending a structure
by E Artikis 10 Sep '21

10 Sep '21

I have a pdb with a fibril composed of three identical chains. I'd like to expand the fibril from three to 15 chains. Is there a way to do this? It's essentially a copy/paste action, but I can't figure it out. Thanks!

2 1