- phenixbb - phenix-online.org

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 13 May '22

13 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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TLS refinement and interpretation of the B factors
by 向嵩 10 May '22

10 May '22

Dear Phenix users, I have sent this message to phenixbb before I subscribed to it and did not see it show up in the bulletin board. I am sending it again and apologize for the possible duplicated messages. I have been trying to understand the B factors generated by TLS refinements and appreciate any help in this subject. In my particular case, I was trying to analyze the dynamics of different portions of a protein molecule by looking at the B factors. The structure was refined with the isotropic B factor and TLS and the TLS groups were determined automatically. After the refinement, I tried to analyze the TLS matrices with phenix.tls_analysis. The analysis failed for many of the TLS groups, the program complains that some of the matrices are not positive semidefinite. I have several questions related to this: 1, in cases like this, can I tweak the initial values of the matrix elements or add constrains to make the TLS refinement results physically meaningful? i.e. the refined TLS matrices can be interpreted in terms of elemental motions. I noticed that Afonine et al mentioned in a recent paper (doi: 10.1107/S2059798318005764) that a large fractions of TLS matrices in the PDB databank can not be interpreted by elemental motions. I wonder if there is a way to make the refined matrices more meaningful in the current implementation of TLS refinement in phenix? 2, what is the "best" B-factor to look at in an analysis for protein dynamics? I am interested in the dynamics of portions of protein that are smaller than the TLS groups. I am guessing that if the TLS matrices are not physically meaningful, one should look at the overall B-factors? If these matrices are meaningful, is it a good practice to look at the residual B factors (overall B-factor minus the TLS contributions)? 3, how to calculate the residual B factors? I could not find a manual for phenix.tls mentioned in the phenix refinement instruction. I tried with the extract_tls=true option with my PDB and got a PDB file with some negative B factors. Is it another sign that the refined TLS matrices are not physically meaningful or am I using the phenix.tls program wrong? Your help in this subject is greatly appreciated. Song Xiang

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Diffraction Methods in Structural Biology - Gordon Research Conference - July 24-29, 2022
by James Holton 07 May '22

07 May '22

Many of you may recall approximately 1000 years ago we were looking forward to getting together for another great Diffraction Methods GRC. Now, after a 4-year break, the meeting is on! https://www.grc.org/diffraction-methods-in-structural-biology-conference/20… It will be in-person at Bates College in Lewiston, ME, USA, on July 24-29 of 2022. Strange how it is strange to be considering meeting in person, but recent GRCs have proven they can be conducted safely. We've learned a lot about viruses in recent years, both in our lives and in our labs. Artificial Intelligence has come a long way, and the role of biological structure, and indeed science in general, is impacting the everyday lives of human beings more than ever before. It is time we got together to talk about all this. Yes, we've gotten a lot of work done remotely, but some things just have to wait until you are face-to-face. Preferably over a Maine lobster dinner. GRCs are not about listening to talks, they are about the discussion that comes after. Newcomers and Veterans sharing and debating ideas until far too late at night. It is my sincere hope that fighting this virus, and looking toward a brighter future, will inspire even more visionary and collaborative ideas for the role structure will play in that future. I can't imagine a better theme of discussion for this next meeting. Some may also recall that in 2020 we were accepting tax-deductible donations to help attendees from underrepresented groups overcome the financial barriers to GRC attendance. Those funds are still available, and donations are also still possible. I ask that applicants who feel they may qualify please self-identify to me, off-list, in an email. It is my goal to bring as many diverse backgrounds and points of view as possible into this meeting, because that is what makes for the most productive discussions. -James Holton MAD Scientist -James Holton MAD Scientist and Chair of the 2020/2022 Diffraction Methods GRC

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get list of missing atoms table in validation
by Wei Wang 06 May '22

06 May '22

Dear all, I would like to get an externally readable list of the missing atoms table in “Summary" session of "Comprehensive validation (X-ray/Neutron)". Currently it seems the information is integrated and clickable only inside the gui window. I want to access the table via sed. Is there a way to extract that table out? Best regards, Wei

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