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Reminder: Phenix user workshop at the ACA2022 in Portland
by Dorothee Liebschner 05 Jul '22

05 Jul '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. *Please note: Registration closes on July 8th!* 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. You need to register for the main meeting in order to participate in the workshop. This is an in-person workshop (no hybrid option). 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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mmCIF output by phenix.refine
by Mark Saper 30 Jun '22

30 Jun '22

Why does .CIF file output by phenix.refine contain all of the -h -k -l reflections. The Bijvoet reflections are already contained in the _refln.pdbx_F_minus column of the +h +k +l reflections. When OneDep at PDB reads in these files, it finds ‘?’ in about half of the reflections, and assigns them a status of ‘x': Warning: (data block=1): 36739 reflections have status assigned as '?' (changed to 'x') Warning: (data block=1): 36739 reflections have wrong status. Not in list(o,f,x,-,<,h,l) Is this the correct behavior? My space group is 19. Thanks, Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505

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3x4 matrix for wwPDB deposition
by Christian Tüting 28 Jun '22

28 Jun '22

Hi Phenix Dev team and mailing list recipients, i have a question regarding the 4x3 matrix in the wwPDB deposition assembly tab. I am wondering, if there is an easier way, than what I am currently doing. This is my current workflow: # get the map symmetry phenix.map_symmetry symmetry=O map.mrc # apply symmetry on monomer phenix.apply_ncs mono.pdb symmetry_from_map.ncs_spec # get biomt from complex phenix.find_ncs apply_ncs.pdb # isolate wwPDB deposition 3x4 matrix awk '{print substr($0, 25)}' find_ncs.biomt > 3x4_matrix And this feels a bit redundant, as I already have the symmetry operation directly from the beginning, but the monomeric localization is missing. Is there an easier way to get the 3x4 matrix? This is still fast, so this is fine, but maybe there is an easier, single line solution. Best Christian

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Running phenix into a M1 apple processor
by Armando Albert 24 Jun '22

24 Jun '22

Dear all, Is there any version of phenix for the new M1 apple processors? Thank you Armando

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Building DNA into the cryo-EM map density
by Yangqi Gu 21 Jun '22

21 Jun '22

Dear PHENIX users and developers, I am currently building a model for a cryo-EM map of a helical complex. I could build the protein easily into the map. However, the map also contains a long chain of DNA density, I am wondering what could be the best way to build this DNA model? I have no previous experience building models with a DNA complex, therefore any suggestion would be helpful! Best. Yangqi -- Yangqi Gu Ph.D. Yale University, West Campus

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ACA hotel block closing June 17
by Anna Gardberg 14 Jun '22

14 Jun '22

Dear Colleagues, The ACA annual meeting in Portland is fast approaching. The meeting will be held from July 29 - August 3, 2022. The hotel room block at the Marriott Downtown Waterfront will be closing on June 17th. Book your room today <https://book.passkey.com/event/50263127/owner/3508/home>! Register for the meeting <https://www.acameeting.com/registration-info> and consider taking one of the workshops <https://www.acameeting.com/workshops> on July 29. WK1: Applications of Small Angle Scattering to Structural Biology: An Introduction WK2: Crystallographic and cryo-EM Structure Solution with Phenix WK3: Cryo-Electron Tomography: State of the Art Methods WK4: Hands-on Single-Particle Cryo-EM Data Analysis with Cryo EDU WK5: CryoEM Sample Preparation Training using Center Merit Badges WK6: Advanced Software Tools for Single Crystal Diffraction WK7: Visualizing Structure WK8: Microcrystal Electron Diffraction (MicroED) If you are already registered for the proximally located M&M conference, you can register for the ACA workshops and/or an ACA one day pass <https://acas.memberclicks.net/index.php?option=com_mcform&view=ngforms&id=2…> . We look forward to seeing you in Portland! The 2022 Annual Meeting Committee

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phenix.douse, resampled map?
by Guenter Fritz 12 Jun '22

12 Jun '22

Dear Pavel, dear all, I was running phenix.douse on a map from resolve. It works very nicely. As far as I understand phenix.douse generates a resampled map with finer grid for water picking. Is there an option to write this resampled map out? Best regards, Guenter

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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 24 May '22

24 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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TLS refinement and interpretation of the B factors
by 向嵩 09 May '22

09 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 05 May '22

05 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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2022 Cold Spring Harbor Macromolecular Crystallography Course
by Paul Adams 03 May '22

03 May '22

Dear Colleagues, The July 15th deadline for applications to the CSHL Macromolecular Crystallography Course to be held later this year, October 10 through October 25 2022, is rapidly approaching. This is a unique opportunity to become expert in the use of crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=22 please pass this on to anyone who you think might be interested and would benefit, especially students and postdocs. This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography, and consists of extensive lectures and practical sessions from experts in the field. The instructor team is: Janet Newman, Tom Peat, Jim Pflugrath, Tassos Perrakis, and myself. We are assisted by world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation (see the course link above for more details). The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. We expect participants to crystallize one or more proteins and determine their structures in a two week period. Students may also work on their own projects, but not exclusively. They will become very well-versed in the theory of diffraction and crystal structure determination, while also having lots of fun. Both synchrotron data collection and in-house diffraction data collection will be used to solve structures. The course will also include the use of computationally predicted structures to aid in solving the crystallographic phase problem. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar and laboratory settings. Please check the above web link for more details. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. The course is supported with funds provided by the National Institute of General Medical Sciences, for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is also provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ] [ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Phenix/Coot issue
by Xavier Brazzolotto 30 Apr '22

30 Apr '22

Dear Phenix and Coot users and developers I've recently observed a kind of conflict between Phenix and Coot. I am using Phenix v1.20.1-4487 and Coot 0.9.8.1 from thee CCP4 8.0 suite under macOS Monterey (v12.3.1). If I launch Coot through Phenix via the « Open in Coot » of a refine job for example (the path to Coot has been defined in Phenix preferences), Coot opens correctly and displays the structure with the « Connected to Phenix tab". However if I wand to do some RSR then I get an error message stating "Refinement setup failure » : « Failed to find restraints for » and a list of the residues involved in RSR. In parallel if I use Coot by itself (launched through the terminal), RSR works well… but upon opening Coot states that there is some "Nomenclature errors » with a list of different residues. I wonder if there would be some conflict between residue libraries between Phenix and Coot ? Just to leet you know I’ve also recently tried to install/comlplie the Coot v1 pre-version to have a loot at it and I do also have libccp4 installed in my Homebrew. Maybe everything comes from that ? Xavier

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3Fe4S clusters in real-space refinement
by Rhys Grinter 27 Apr '22

27 Apr '22

Hi PHENIX BB, I'm currently refining a structure with 3Fe4S clusters into some high resolution cryoEM maps (1.57 Ang). However, refinement messes up the Fe4S cluster, by moving the existing Fe and S atoms into the wrong positions in the density. Is anyone aware of this issue and/or knows of a simple way to prevent this from happening? Cheers, Rhys -- Dr Rhys Grinter Lab Head Molecular Physiology of Microbial Pathogens (MP2) Lab Monash University +61 (0)3 9902 9213 +61 (0)403 896 767

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Re: [phenixbb] NaN of AlphaFold
by Randy John Read 26 Apr '22

26 Apr '22

Did you try looking at a surface representation of the structure? The one that Pavel generated from a more simplistic random sequence looked vaguely plausible as a chain trace, but had very large cavities when viewed as accessible surface, e.g. in ChimeraX. Randy > On 24 Apr 2022, at 01:36, James Holton <jmholton(a)lbl.gov> wrote: > > I downloaded all sequences from the PDB to do a frequency analysis, which I think will enable a more sophisticated "random peptide" than giving all 20 amino acids equal likelihood with no neighbor correlations. Turns out the most common heptapeptide in the PDB is: > XXXXXXX > > because, apparently, NCBI lists gaps like this. If I eliminate "X", the most common heptapeptide is: > > SHHHHHH > > Right. His tags. If I eliminate those, the next one is: > GLVPRGS > thrombin cleavage site. Ugh! > > Cleaving off those, the next one is: > AAAAAAA > apparently also used to denote unknown amino acids. > > Ignoring those, the next one is: > YFPEPVT > this is from the human antibody heavy chain. Thousands of those in the PDB. This made me realize that there is going to be a lot of "homology bias". > > I next tried the NCBI refseq_select to try and get something non-redundant, and then I get: > GSGKSTL > lots of ABC transporters. >10k of this sequence in the db. > > On the other hand, of the ~330e6 heptapeptide sequences I'm looking at, 52% of them only appear once. Another 19% of my list of unique sequences occur twice, 9% occur 3x, etc. It is a VERY steep curve. Only 4% of my sample sequences occur more than 10 times, and 0.05% occur more than 100x. I never thought of the PDB this way, but I take this as indicative of how much repetition there is in the sampling. Perhaps I need to brush up on my statistics, but I did not expect this. > > So, I said "heck with it" and simply extracted all heptads that only occur EXACTLY ONCE in the PDB. There are 7.4e6 of them. I chose one at random as the starting 7 residues: FLACISE (from 6ekr). Rather than simply appending random heptads, I took the final ISE and extracted all one-off heptads that begin with ISE. There are 1905 of those. I chose one at random: ISENDGN (from 6ixy). I then extracted heptads beginning with DGN, etc. Final sequence of randomly-assembled yet abbuting heptads from random places in the PDB is then: > > > random1 > FLACISENDGNDGDKSNLAQDTDLALGTWVRDISIALRSGFIAEEYPAWWKESVVPYYNQLNGN > DIEHSHSALLPTGIYFLEIPLVGTRDVALDTEGETTEEAFRHLDGIVGHPIVIGRRAADGGPLVIRGL > NEVLLRLSEVYNAWKLLKVQEILKGLEAYNRAMDYETILREGTWKPAGYTPNALAGGAQCGNAD > IVNERIISDGVEASQLATLERRENRALQTALEIENGELEQKWGRLPSAXPAVERQRYRGPSTATW > EGFSTDGRFPSEVDIFDRETLDGVEGLAKDVEALKGVLMGLFAPYWKWCTHNCIGYAARFVALN > KAIRTALTFARTHSNNETIHNEVVGMIPDIDIAVSDINSQEYTKTRSERQGGVLKEHLNALNAKIEPS > VNLKVSA > > A quick BLASTP shows a surprisingly high homology match: > <o4TgiNP8vaFOcUkl.png> > > I mean... not great, but higher than I'd expect for "completely random" ? > > > The alphafold2 colab result looks like this: > > > <rHffn0Fa0WfwR4Yg.png> > > So still lots of helical content. This shape makes me want to make this sequence and see if it folds. It probably doesn't. But if this thing weren't red I'd wonder. > > Discuss? > > -James > ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

2 1

Refining cyclosporin A
by Armando Albert 22 Apr '22

22 Apr '22

Dear All, We are trying to refine a protein complex with cyclosporin which is a non conventional cyclic peptide. I wonder what is the best strategy to build the cif file. Shall we define the cif file for individual non-conventional amino acids and then link them or shall we define the whole structure as an individual ligand? Does any one have the corresponding cif file? Armando

3 2

Validation of structure with modified residue
by Xavier Brazzolotto 21 Apr '22

21 Apr '22

Dear Phenix users, I don’t know if my problem is related to Phenix but for information I’m running Phenix 1.20.1-4487 under MacOS 12.3.1. I’ve finalized a structure where a ligand covalently modified the protein. I’ve generated the modified residue (named SLG for serine modified by ligand). For this I’ve generated the molecules in SMILES and used eLBOW to generate the restraints. Then I’ve modified the cif file defining the molecule as a L-peptide and replacing the atom names of the Serine part (CA, CB, OG, C, O, N, and OXT) In coot (from CCP4 : 0.9.6 EL), I’ve used the modified cif file and it allowed merging of the modified residue into the polypeptide chain as expected and further refinements went without any issue in Phenix (providing the modified cif file of course). Everything seems well interpreted. So far so good. However, now I would like to validate the structure and both Phenix validation tool and the PDB web server do not accept the final cif file. Checking this file I’ve noticed that the protein seems split into 3 pieces (chain A, first residue up to the one before the modified residue; chain B the modified residue by itself described as HETATM and chain C the rest of the polypeptide up to the C-ter). The PDB file presents only one chain A for the whole protein with the modified residue... I don’t know if this is an issue with Phenix generating this final cif file in this specific case or if I need to modify this final file by hand ? Any help is welcome. Thanks Xavier

4 9

ligand at two-fold
by Patrick Loll 14 Apr '22

14 Apr '22

Hello all, I have a dimer in which the two protomers are related by a crystallographic 2-fold. There is a peptide ligand that sits in the interface between the two protomers. This means that the ligand will be present in two orientations, and I’ve set the occupancies to 0.5. However, the ligand is pushed out of density during refinement, presumably because orientation #1 is repelling orientation #2 (to be clear, orientations #1 and #2 are symmetry mates). To deal with this, I include a parameter file in the GUI that contains the following instruction: custom_nonbonded_symmetry_exclusions = "chain X” [where chain X is the peptide ligand] However, the refinement fails, with the following error message: "Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions." This would seem to imply that the custom_nonbonded_symmetry_exclusions command is obsolete, but it’s still found in the list of all available keywords (?). Any help would be welcome. Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA pjl28(a)drexel.edu pjloll(a)gmail.com

2 1

Error from exceeding max reasonable bond distance
by Mullins, Elwood A. 13 Apr '22

13 Apr '22

I’m having an issue with a real-space refinement job crashing after giving the following error: "RuntimeError : Bond distance > max_reasonable_bond_distance: 62.8014 > 50". I found mention of this problem in a post from 2017. I tried the recommended solution (setting the max reasonable bond distance to 999), but that caused the job to hang. I also tried clicking “proceed with excessive length bonds”. That didn’t make a difference; I received the same error message. I ran validation on the model. There are no bond length outliers and only minor other issues. Any help would be greatly appreciated. Thanks, Elwood

2 1

The lowest resolution score X-ray statics resolution bin is lower than overall datasets.
by Takebe Katsuki 11 Apr '22

11 Apr '22

Dear all, I am working on a 20 KD protein and We scaled the data sets 1.6Å. The lowest resolution score X-ray statics resolution bin is lower than overall datasets. Is this seriously problem? and How do I solve the problem? Could you give me some advice on this problem? DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : 1.600 RESOLUTION RANGE LOW (ANGSTROMS) : 44.488 　 [cid:[email protected]]

2 1

2022 ACA session on AI predicted Models in Structural Biology/Crystallography
by Aaron Brewster 11 Apr '22

11 Apr '22

Hi all, we'd like to call your attention to the upcoming session at the 2022 ACA on the use of AI predicted Models in Structural Biology/Crystallography. We'd like to invite abstract submissions to this session from people, including early-career scientists, who have done difficult or interesting work using these AI predicted structural models, such as from AlphaFold2 and RoseTTAFold. We are very excited to hear what people are using these tools for and how the future might unfold in this new world of AI-aided structural analysis and design. Remember that the deadline to submit an abstract for talks is April 15, 2022@ 11:59 PM ET. The full abstract for the session is below. Thanks, -Aaron Brewster and John Moult Prediction of 3D protein structure by AlphaFold2 and RoseTTAFold has achieved revolutionary accuracy using new AI methods. These programs can accurately predict the 3D structure of many proteins from 1D amino acid sequences, opening up a vast array of exciting new experiments and challenges for researchers. In this session we will explore current applications of these structures in molecular replacement, cryo-EM fitting and refinement, structure-based drug design, and tomography. We will explore what kinds of new and difficult methods have been enabled and what remains difficult. Other topics may include how error estimates on AI protein models can be incorporated into these methods, progress in modeling of protein complexes, implications of AI structures on protein design, the generation and use of structure ensembles, and new data analysis best practices that need to be developed as the use of computer-generated structures becomes more common. Sponsored by the BioMAC and Best Practices for Data Analysis and Archiving SIGs

1 0

The lowest resolution score X-ray statics resolution bin is lower than overall datasets.
by Takebe Katsuki 11 Apr '22

11 Apr '22

Dear all, I am working on a 20 KD protein and We scaled the data sets 1.6Å. The lowest resolution score X-ray statics resolution bin is lower than overall datasets. Is this seriously problem? and How do I solve the problem? Could you give me some advice on this problem? DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : 1.600 RESOLUTION RANGE LOW (ANGSTROMS) : 44.488 　 [cid:[email protected]]

2 1

Fragment-based drug discovery session at ACA 2022
by Tanner, John J. 08 Apr '22

08 Apr '22

As many of you know, the 2022 ACA meeting will be held in Portland, OR on July 29 to August 2. I would like to draw your attention to the session on fragment-based drug discovery and invite you to submit an abstract for an oral presentation. We welcome contributions from students as well as PIs. The Abstract deadline is April 15. https://www.acameeting.com/ Session details: 3.2.2 Fragment Based Drug Discovery 8/1/2022 @ 2:00:00 PM - 5:00:00 PM Sponsoring SIG(s): Industrial Co-Sponsoring SIG(s): BioMac Session Chair(s): Matt Clifton, Jack Tanner Fragment Based Drug Discovery (FBDD) utilizes small molecule compounds to help identify starting points in the drug discovery process. This process allowed for the discovery of lead compounds for difficult protein targets with small/shallow pockets or protein-protein interactions. In contrast to other screening techniques such as High-Throughput Screening (HTS) or DNA-encoded Libraries (DEL), FBDD utilizes small libraries of molecules (< 2000) with molecular weights less than ~200 Da. FBDD has been key in the development of multiple approved drugs and dozens of other drugs in clinical trials. This session will focus on the biophysical and structural techniques used in FBDD to identify initial starting points, optimization by fragment growing/linking, and the route to lead optimization. -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

1 0

CCN submissions and current issue
by Nigel Moriarty 05 Apr '22

05 Apr '22

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 1 JUN 2022. 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. Current Issue: January 2022 Full issue <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> Articles: - Extreme backbone outlier patterns when AlphaFold gives up <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> - Difference Density Tracer: A Tool for Rapid Visualization of Difference Densities in Proteins to identify Dynamics <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> Fitting Tips: - Fitting tips #22 – Places where you should never fit a cis-nonPro peptide <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> 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

Question about RMSD vs e/A^3
by Vatsal Purohit 30 Mar '22

30 Mar '22

Hi all, I had a question about comparing structures based on RMSD comparisons vs e-/A^3. While the former seems to be more frequently used in structural studies with a standard value of 1.0 rmsd for 2Fo-Fc and 3.0 rmsd for Fo-Fc, there are differences in RMSD based on resolution. Hence, I wanted to ask if e-/A^3 could be a more appropriate comparison for looking at differences in electron density in a ligand-binding site between 2 structures of the same enzyme? So, here you would try and set e-/A^3 of all the maps (2Fo-Fc and Fo-Fc) to the same value. The structures I’m referring to are between 2-2.5 angstroms in resolution. I have also worked with the map sigma level comparison tool on PHENIX and wanted to know if that might be an alternate way to compare maps in 2 structures accordingly. Regards, Vatsal Post-doctoral fellow, Davis Lab, Emory University vatsal.purohit(a)emory.edu <mailto:[email protected]> | 346-719-9409

4 3

Phenix.refine question
by Mark Saper 23 Mar '22

23 Mar '22

Laurie, Really bizarre. The experts will have more info, I hope. When you model the Tyr in the posiive density, is the geometry satisfactory (including main-chain)? If so, then you might try turning off real space refinement and see what happens. Check the occupancies of the Tyr also. -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

2 1

Phenix.refine question
by lbetts0508 18 Mar '22

18 Mar '22

I am refining a small protein crystal model with 1.3 A data, there is a Tyrosine that won't stay put where it looks to me it should go (see below in it's original position, in the negative density; I moved the ring into the positive Fo-Fc density). After I move it into the positive density, save the coordinates, and do another refinement with the new coordinates, I find it right back in the negative density, even if I only refine ADP or OCC. Is there some trivial reason this is happening, or can I tell it to not refine that residue? https://docs.google.com/document/d/1RkZSH312q2Pimxb9gKLjibm1XbpsVpyzmrX4wGx… THanks Laurie Betts

2 1

Postdoctoral position in the MRC Laboratory of Molecular Biology
by Roger Williams - MRC LMB 16 Mar '22

16 Mar '22

Our group has an opening for a postdoctoral fellow to be funded on a Cancer Research UK programme aimed at understanding lysosomal control of cell proliferation and stress responses in cancer cells. The programme involves cryo-electron microscopy, X-ray crystallography, H/D exchange mass spectrometry, molecular dynamics as well as other biophysical and biochemical approaches. The post will focus on the reconstitution of large signalling assemblies that detect nutritional and stress signals on and off membranes. The candidate will join a vibrant team of researchers investigating structures, regulation, kinetics and dynamics of phosphoinositide 3-kinase family members reconstituted with their regulators on membrane surfaces. This programme concerns regulation of the lipid kinase VPS34 and protein kinase mTOR and ATM-containing complexes. The research combines biochemical, biophysical and cell biological methods with structural approaches. This is a unique opportunity to play a major role in exciting programme, introduce new ideas, and disseminate research results, while working in a collaborative and supportive environment. The position is available immediately, with an application closing date of 11 April 2022. For more details, please see https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog…> Please contact Roger Williams at rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>, if you have any questions. Dr. Roger Williams, FMedSci, FRS rlw(a)mrc-lmb.cam.ac.uk MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Phone: +44 1223 267094

1 0

Molecular replacement of cyclic polypeptide with non-standard amino acid
by Ariela Samantha 09 Mar '22

09 Mar '22

Dear all, I have collected an XRD data from a crystal of cyclic polypeptide with non-standard amino acid (2,4-diaminobutyric acid). Is it possible to solve the structure by molecular replacement? Or does anyone have any suggestion for solving the structure? Thank you very much for your kind help. --- Best regards, Ariela Samantha PhD Candidate Department of Structural Biology School of Molecular Sciences The University of Western Australia Bayliss Building room 4.26 Phone +61 8 6488 ext. 3163

2 1

Error message on minimization global
by Abhipsa Shatarupa 08 Mar '22

08 Mar '22

Hello, I am a beginner in phenix. Currently, I am running minimization global under real-space refinement. The input files for this job are a .pdb file generated from rigid-body refinement and a .ccp4 map. I end up receiving the following error message (image attached -Error file). The output log file gives me the description of the number of atoms and the atoms responsible for generating the error (image attached – atoms file). I ended up finding a couple of Q/A on a similar error message, but I am not sure how to generate the CIF file to overcome the problem using eLBOW? Could someone please help me resolve this issue? Thanks in advance, Abhipsa

2 1

XChem access: Diamond AP32 Call for Proposals open until 30 March 2022
by Fearon, Daren (DLSLtd,RAL,LSCI) 08 Mar '22

08 Mar '22

Hi all, Friendly reminder that the Diamond AP32 call for proposals (which includes XChem access between October 2022 and March 2023) is open until Wednesday 30th March at 17:00hrs UTC/GMT+1. Please check our webpage<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/XChem-Applicati…> for more details and if you have any questions about applying then do get in touch. Cheers, Daren Dr Daren Fearon (he/him) Senior Beamline Scientist (XChem) Diamond Light Source Ltd Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE Tel: 01235 778936 Mobile: 07425638147 Email: daren.fearon(a)diamond.ac.uk<mailto:[email protected]> Web: www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html<http://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html> [https://gallery.mailchimp.com/3de94671e0e91f373e1995d94/images/557065e4-53a…] Reminder: Diamond – AP32 Call for Proposals Dear Colleague, This is a gentle reminder that our call for proposals for AP32 is open and the deadline for this call is Wednesday 30th March at 17:00hrs UTC/GMT+1. The period will cover October 2022 to March 2023. Please note that as this is in working hours the call will be closed at this time. A table of instrument access is given here<https://www.diamond.ac.uk/Users/Apply-for-Beamtime.html>. Users from the EU: Submitting proposals and visiting Diamond post-Brexit Users from European organisations continue to be welcome to submit proposals to Diamond. The same funding policy and procedure for expenses continue to be in place for any visit to Diamond as was in place before Brexit. You can find our expenses procedure here.<https://www.diamond.ac.uk/Home/Legal-and-Compliance/Procedures/Financial-Su…> Proposal Information The science case and reporting templates have been updated. You are strongly encouraged to use the most up-to-date template available for download in the User Administration System. Experiments that can be completed remotely or by mail-in should be highlighted. Please refer to the relevant information that each of the beamlines have published. You will find relevant information under each instrument’s specific information here.<https://www.diamond.ac.uk/Instruments.html> Do discuss your planned work with our instrument scientists and submit all proposals to UAS<https://uas.diamond.ac.uk/>. In addition, please ensure that any outstanding reports are submitted, and that your publications related to your previous beamtimes are in our database<http://publications.diamond.ac.uk/> as the peer review panel will take these into consideration during the review. A number of additional instruments will be taking submissions for proposals: I06<https://www.diamond.ac.uk/Instruments/Magnetic-Materials/I06.html> - Laser-PEEM/LEEM Facility for Multidisciplinary Nanoscience Imaging: A new multidisciplinary nanoscience imaging facility, using PhotoEmission Electron Microscopy (PEEM) and Low-Energy Electron Microscopy (LEEM), will be available for peer-reviewed access starting in AP32 (from October 2022). PEEM gives nanoscale insights into the magnetic properties of materials whilst LEEM provides detailed nanoscale structural insights through full-field imaging combined with spatially resolved Low-Energy Electron Diffraction (micro-LEED). The facility combines PEEM/LEEM with a continuous wave (CW) laser (Laser-PEEM/LEEM) providing high spatial resolution with probing depths ranging from less than a nanometre to tens of nanometres. To submit a proposal please select I06 in submission process. Further details are available from Dr. Sarnjeet Dhesi (dhesi(a)diamond.ac.uk<mailto:[email protected]>). The multidisciplinary Laser-PEEM/LEEM facility is funded by Diamond Light Source and the Engineering and Physical Sciences Research Council (EPSRC Grant: EP/V029258/1) and is being developed in collaboration with the Central Laser Facility, the University of Oxford, the University of Cambridge, the University of Nottingham and University College London. ________________________________ Diamond's new Active Materials Laboratory<https://www.diamond.ac.uk/Science/Integrated-facilities/active-materials-la…> (AMLab) is in the process of being fitted out and is now ready for use. Users who want to use this facility in their proposals will be able to select it as an instrument in UAS<https://uas.diamond.ac.uk/>. ________________________________ DL-SAXS<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> - The Offline SAXS instrument, Xeuss 3.0<https://www.xenocs.com/saxs-products/saxs-equipment-xeuss/>, from Xenocs<https://www.xenocs.com/>, has been delivered with both Excillium Gallium MetalJet and Molybdenum Microsource options. The instrument has a set of sample holders<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> available for use. Please discuss any ideas for Sample Environment driven experiments with a member of the team<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> before submitting. ________________________________ B07<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07.html> – When submitting proposals for B07 the award will be assigned by the beamline staff<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07/Staff.html> to the branch line (B07-B or B07-C) which is optimal for a given experiment. Please select B07 when you submit your proposal with a view to beamline staff determining which of the two branch lines, B07-B and B07-C, will be the optimal choice. Applicants are encouraged to discuss the options with the beamline staff before submission and will be able to express their preference in the “beamline questionnaire” part of the proposal form. ________________________________ DIAD<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/DIAD.html> - The Dual Imaging and Diffraction (DIAD) beamline is a dual beam X-ray instrument for imaging, diffraction and scatterin g, which operates at energies of 7-38 keV. Information and questions to consider when writing the proposal can be found on the DIAD web-pages. ________________________________ I08<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/I08.html> has extended its portfolio with a new instrument for soft X-ray ptychography (I08-1). When submitting proposals for I08 the award will be given for that instrument with a view to beamline staff determining which of the two instruments will be the optimal choice for a given experiment. Please contact Burkhard Kaulich<mailto:[email protected]> (I08 PBS) for further information. Best wishes, Diamond User Office [Diamond Light Source Logo]<https://www.diamond.ac.uk/> Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire. [Follow Us on Twitter]<http://www.twitter.com/DiamondLightSou> [Website]<https://www.diamond.ac.uk/> Copyright © 2022 Diamond Light Source, All rights reserved. Our mailing address is: Diamond Light Source Diamond House Harwell Science & Innovation Campus Didcot, Oxfordshire OX11 0DE United Kingdom Add us to your address book<https://diamond.us20.list-manage.com/vcard?u=3de94671e0e91f373e1995d94&id=7…> You are receiving this email because you are registered in our User Administration System (https://uas.diamond.ac.uk). If you would like to opt out of future bulk emails, please click unsubscribe<https://diamond.us20.list-manage.com/unsubscribe?u=3de94671e0e91f373e1995d9…>. Please note that unsubscribing from this mailing list will not stop you from receiving operational emails related to your upcoming visits or essential information related to your account. If you wish to update your personal information, please do so directly in the User Administration System (https://uas.diamond.ac.uk<https://uas.diamond.ac.uk/>). For more information about our privacy policy, please visit www.diamond.ac.uk/Legal<http://www.diamond.ac.uk/Legal.html>. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

1 0

Online Workshop Series on Structural and Crystallographic Databases -- Registration Open
by Mitchell D. Miller 03 Mar '22

03 Mar '22

On behalf of The U.S. National Committee for Crystallography (USNC/Cr) of the National Academies of Sciences, Engineering, and Medicine, I am happy to announce that registration is now open for "EXPLORING STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES". The topics will focus on using, developing, and maintaining crystallographic and structural databases- encompassing macromolecular, small molecule, and powder diffraction. We will open the series with a keynote delivered by John Helliwell (IUCr Chair of the Committee on Data) on March 21, 2022 followed by 10 one-day and two-day workshops focused on 8 different structural and crystallographic data resources. An overview of the program can be found in the attached PDF. Graduate students, postdoctoral fellows, faculty members and researchers in any of the crystallographic, diffraction, and imaging sciences affiliated with the International Union of Crystallography (IUCr) are encouraged to register and participate in the training sessions that interest them. Registration for this online series is free. To read more about each session and to register, please visit: https://www.nationalacademies.org/our-work/exploring-structural-database-us… The details about each session can be found by clicking the event pages along with a registration link allows one to register for any combination of the 1 and 2 day sessions (each meeting for 2-4 hrs/day). The workshop series is sponsored by the National Institute of Standards and Technology (NIST). For more information, please contact Ana Ferreras, Telephone: (202) 334-1697 Email: aferreras(a)nas.edu[1] Sincerely, Mitch Links: ------ [1]

1 0

Coot opening problem
by Afshan Begum 03 Mar '22

03 Mar '22

Hi Expert, I am refinening my strcuture on phenix , Could you kindly suggest me why after refinement in phenix (version i used 1.9-1692, Mac operation system) COOT does not open up by clicking on COOT button.Its seems open but only black screen (or blank window) come up without out any data, As previously always its open very smoothly , so now i have to open all files manually every time. Best Regards =============================== Afshan Begum

1 0

Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

Thanks to Tom the issue is resolved. If I examine the MTZ file with phenix.mtz.dump the angles are in degrees as they should be. For some reason CCP4 ViewHKL program shows them in radians although they are stored internally as degrees. > The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? > > -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

1 0

Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Call for Topical review articles for Acta Cryst F Structural Biology Communications
by John R Helliwell 25 Feb '22

25 Feb '22

Dear Colleagues, We draw your attention to our call for Topical review articles for Acta Cryst F Structural Biology Communications described here:- https://journals.iucr.org/f/issues/2021/11/00/me6156/index.html We welcome your proposals. Best wishes, John, Mark and Janet John Helliwell, Mark van Raaj and Janet Newman Emeritus Professor John R Helliwell DSc

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General interest
by John R Helliwell 02 Feb '22

02 Feb '22

Dear Colleagues, I imagine you would be interested in the book “Collecting Experiments. Making Big Data Biology” which I have reviewed here:- https://journals.iucr.org/j/issues/2022/01/00/xo0187/index.html My book review is open access. I have dedicated my book review to John Westbrook. Best wishes, John Emeritus Professor John R Helliwell DSc

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PhD fellowship at NC State & Oak Ridge National Laboratory
by Meilleur, Flora 25 Jan '22

25 Jan '22

Thank you for sharing the following PhD opportunity with interested students! Best wishes, Flora PhD fellowship in Structural Biology of Metalloenzymes at NC State & Oak Ridge national Laboratory A Ph. D. research fellowship (up to 5 years) in enzyme chemistry is available with Dr. Flora Meilleur. The position is joint between North Carolina State University, the Ph. D. granting institution where the Ph. D. candidate will complete the program core coursework, and Oak Ridge National Laboratory, where research activities will be performed. The project will focus on lytic polysaccharide monooxygenase, a class of copper containing metalloenzymes involved in biomass oxidation. High resolution X-ray and neutron crystallography will be used primarily to study the enzymatic mechanism. The project will involve collaborations to include spectroscopic and biophysical methods as well as computational approaches. Key publications on the topic include (complete list here<https://scholar.google.com/citations?user=i0aLPhYAAAAJ&hl=en>): Schröder G.C., O'Dell W.B., Webb S.P., Agarwal P.K., and Meilleur F. (2021) Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. ChemRxiv. 10.26434/chemrxiv-2021-n4c1x<https://chemrxiv.org/engage/chemrxiv/article-details/61b3cdd8689c875d6adea9…> O'Dell W. B., Aggarwal P., Meilleur F. (2017) Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew. Chem. Int. Ed. 56:767-770<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340418/> The candidate should hold a degree in chemistry or biochemistry. Prior experience in molecular biology, protein expression, or protein purification is an advantage. The position is available now and applications are welcome until the position is filled. Interested candidates must email a detailed CV, a letter of motivation and the name of three scientists for reference to Flora Meilleur<mailto:[email protected]?subject=Application%20to%20NC%20State%20/%20ORNL%20PhD%20Fellowship> prior to applying to the Graduate Program in Biochemistry at NC State. For further information about the position, interested candidates can contact Flora Meilleur<mailto:[email protected]?subject=Questions%20about%20NC%20State/ORNL%20PhD%20Fellowship>. Further information about the NC State Biochemistry graduate program here<https://cals.ncsu.edu/molecular-and-structural-biochemistry/>. Further information about the neutron facilities at Oak Ridge National Laboratory here<https://neutrons.ornl.gov/>.

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refining a covalent-bound ligand (part 2)
by Sergio A. Sampieri 22 Jan '22

22 Jan '22

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refining a covalent-bound ligand (part 2) (try 2)
by Sergio A. Sampieri 22 Jan '22

22 Jan '22

Hi all, hope this message finds you well. As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand. The link shall be made between a carbon atom that is double bonded to an oxigen “SMILES C1=CC=C(C=C1)C=O” and the SG group of a Cys residue. I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different approaches during refinement, (Automatic Linking parameters, Atom selection, acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”). I readed in the phenixbb that this was solved by changing the nature of the ligand ( http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html), but is not the way I would like to follow. Any suggestions or ideas would be greatly appreciated, thanks a lot for your time. Stay safe. -- “I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.” John J. Holland Biól. Sergio Aguirre Sampieri

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AlphaFold changes everything": new lecture on the Phenix tutorials channel
by Dorothee Liebschner 22 Jan '22

22 Jan '22

Hi everyone, I hope you will like "AlphaFold changes everything <https://www.youtube.com/watch?v=9IExeA_A8Xs>", the latest addition to the Phenix tutorials channel at www.youtube.com/c/phenixtutorials. In this full-length lecture, Tom Terwilliger shows how AphaFold models are great hypotheses that can help you jump-start structure determination by X-ray crystallography and Cryo-EM. The talk is from the ReNaFoBis.FRISBI webinar series organized by Jean Cavarelli (https://www.renafobis.fr/seminaires-web-renafobis). 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

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