- phenixbb - phenix-online.org

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

10 Jun '22

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

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Postdoctoral position in Manchester
by Harshwardhan Poddar 08 Jun '22

08 Jun '22

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

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

06 Jun '22

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

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Problem with rebuild_predicted_model
by Andrei Moiseenko 04 Jun '22

04 Jun '22

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

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custom planar restraints ?
by Guenter Fritz 30 May '22

30 May '22

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

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Phenix user workshop at the ACA2022 in Portland
by Dorothee Liebschner 25 May '22

25 May '22

Dear Colleagues, The Phenix developers will be holding a day-long satellite workshop on July 29th, prior to the ACA meeting in Portland, Oregon. This Phenix user workshop will focus on using predicted models for crystallography and cryo-EM The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. Topics will cover aspects of macromolecular structure determination in Phenix. For registration, see the ACA 2022 website: https://www.acameeting.com/aca-wk2 . Lecturers: Pavel Afonine, Dorothee Liebschner, Billy Poon, Tom Terwilliger Looking forward to seeing you there! The Phenix team Detailed Program: 8:00 Welcome: Introduction to Phenix, Introduction to the GUI, set up Phenix 8:45 Overview -- Strategy for X-ray or Cryo-EM structure determination using AlphaFold models (lecture) 9:15 Predicting your structure with AlphaFold and trimming it with ProcessPredictedModel (demo) 9:45 Solving an X-ray structure automatically by MR with PredictAndBuild (demo with pre-computed data) 10:15 Break 10:45 Evaluating X-ray data with Xtriage 11:00 Xray refinement (lecture) 11:30 Xray refinement with AlphaFold reference models (demo) 12:00 Lunch 13:00 Ligands (lecture & demo) 13:30 Cryo-EM Data evaluation with Mtriage (short lecture & demo) 13:45 Cryo-EM map manipulations, map improvement with LocalAnisoSharpen and ResolveCryoEM (demo) 14:30 Break 15:00 Automatic cryo-EM map interpretation with PredictAndBuild (demo with pre-computed data) 15:30 Cryo-EM refinement (lecture and demo) 16:00 Model validation (lecture & demo) 16:30 Q&A 16:50 finish: workshop survey and wrap up -- Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Exciting post-doc position available on DNA transcription and conjugation at the ALBA synchrotron
by Roeland Boer 17 May '22

17 May '22

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

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

14 May '22

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

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

14 May '22

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

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

12 May '22

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

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