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AmberPrep not prepping
by Nikolas 01 Aug '26

01 Aug '26

Hi everyone, New to this forum, I usually lurk in the European counterpart, which makes me a novice on the many tools of phenix. I’m trying to refine a low-res structure that has a strong signal in the active site, for which I modeled a putative reaction intermediate. However, this molecule is both linear and long (14C) and thus very flexible, and only the part nested shows clear electron density, leaving out 4-5 atoms. When I run refinement, seems like the molecule gets crammed into the available density and this strains geometry. A clipped version of the ligand fits the density nicely and doesn’t appear strained. Hence, my attempt to use Amber on phenix.refine. AmberPrep gives back an error saying that the file is empty and the leap.log complains both about the ligand and a distance in the protein. The ligand was generated with eLBOW using SMILES and AM QM 1, while the enzyme is split in an alpha and beta subunits each monomer due to autoproteolytic activation and the in-between is highly flexible and thus absent from the model. Is there a way to fix this? Do I have to split each subunit into different chains in the PDB file (e.g. diner with ABCD chains instead of just AB)? Thanks! Best, Nikolas

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RSR of tetramer, rotamers of different protomers/chains change
by skaruppan＠kumc.edu 29 Jul '26

29 Jul '26

Hi All, I want to apologize in advance for such a basic question. I'm working with a tetrameric protein and am attempting to build a model. The resolution estimate of the map determined by cryoEM is 3.8A. Some parts of the map are great while some other parts not so much. To assist with modelling the tetramer, I used the local refinement of one protomer to build a protomer model (one chain). I then used that protomer model as a template to build the full tetrameric model, and I make sure that each protomer is exactly the same (using ChimeraX or coot) by copying one chain over to the next and making certain they are all exact copies of one another. When doing real space refinement in phenix 2.0-5936 of the tetramer model, I end up with good statistics and what I think is a complete model. RCSB/comprehensive cryoEM validation also seem to complement my modelling. However upon closer inspection I noticed that many rotamers across the model are different, for example Chains A and B will have a Gln in one position, while chains C and D will have rotamers in totally different positions. These rotameric seem to happen in substandard regions of map quality. My understanding is that all the protomers in a C4 channel should look exactly the same. To attempt to rectify this problem I've made sure that NQH_flips is off (rotameric changes still happen with many different residues), as well as tried using reference restraints of my protomer, or NCS constraints of one protomer (these options results in a degradation of model quality). I'm missing or misunderstanding something here (or maybe a combo of both), and I was wondering if there was any advice from the community on how to proceed. Kind Regards, Seb

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Deadline Extended: Macromolecular Crystallography - CSHL Course October 2026
by Paul Adams 23 Jul '26

23 Jul '26

Dear Colleagues A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 11-27th this year (pleased see below for more details, with an extended deadline of August 14th). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. 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. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Many applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams, Dorothee Liebschner, Janet Newman, James Pflugrath, Tom Peat <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> October 11 - 27, 2026 Applications Due: August 14 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia X-ray crystallography has been the cornerstone of structural biology for half a century and remains the technique of choice for atomic resolution understanding of macromolecules and for structure guided drug discovery. This course combines laboratory and computational instruction to train course participants in the major techniques used to determine three-dimensional structures. It is designed for scientists with a working knowledge of protein structure and function, but who are new to macromolecular crystallography or who wish to increase their in-depth knowledge of macromolecular crystallography. The advent of methods for the accurate prediction of protein structures is accelerating crystallography experiments, and the course will train researchers in how to best use these models. Topics Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) Participants have extensive hands-on training in well-equipped labs in how to crystallize proteins and determine crystal structures by several methods, while learning through lectures on theory and methods. Both basic and advanced subjects are covered during lectures, which are given by leaders in the field. Informal discussions behind the techniques are frequent and students are expected to pose questions to be answered in interactive sessions. For further information and to apply please visit the Macromolecular Crystallography course website. <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road | Cold Spring Harbor, NY 11724 US Unsubscribe <https://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA==&c…> | Update Profile <https://visitor.constantcontact.com/do?ch=5f75c3d0-c591-11e3-b735-d4ae52843…> | Constant Contact Data Notice <https://www.constantcontact.com/legal/customer-contact-data-notice> -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.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 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 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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Searching for a PhD position
by Mohak Udiniya 19 Jul '26

19 Jul '26

Dear PhenixBB readers, I am searching for a PhD position in a lab that uses structural biology techniques (predominantly crystallography and electron cryomicroscopy) to investigate protein biochemistry, structure, catalysis and synthesis. I would also be interested in labs that conduct various structural studies on viral and bacterial(archaea) proteins. My goal is to conduct fundamental interdisciplinary research using structural biology as my main field of study. Brief CV: - Postgraduate in Cancer Cell and Molecular Biology from University of Leicester. - Extensive research experience in biophysical techniques with hands-on training in crystallography, Powder XRD, FT/IR and spectrophotometry. - Previous experience in studying Ascorbate Peroxidase (Haem peroxidase) biochemistry. - Very well trained in molecular biology, protein expression and purification. I am an international student not belonging to the UK/EU-region and would prefer a position that is fully funded. The location of the lab is not a constraint and, I would be glad to contribute to any lab that is conducting exciting research in the field of structural biology. I would like to thank all the readers for their time and consideration. Best wishes, Mohak Udiniya

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CBMS Lecture Series - Padua - 22 July 2026
by Stojanoff, Vivian 14 Jul '26

14 Jul '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Ricardo Padua Howard Hughes Medical Institute The Scripps Research Institute WEDNESDAY, July 22, 13:30 (EDT) "Visualizing enzyme catalysis through X-ray crystallography" Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/sQhXauTtSGa3iwB6X-tQ3g Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Understanding how protein motions contribute to enzyme function remains a central challenge in molecular biology. How are motions occurring on different timescales connected, and how do they contribute to catalytic efficiency? Have proteins evolved to preferentially access the conformational substates required for function? Recent advances in structural biology, protein engineering, and X-ray crystallography are providing new insights into these questions. Studies of directed evolution have revealed how enzyme dynamics can be optimized to produce highly efficient artificial catalysts, while developments in crystallographic data collection have enabled visualization of the molecular mechanisms underlying temperature adaptation in exceptionally proficient enzymes. Together, these findings highlight the intimate relationship between protein motions, evolution, and enzymatic function. =================================== Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973

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PDB deposition question: processed data in P6₃22, refined model in P6₃
by fbetulertem＠gmail.com 14 Jul '26

14 Jul '26

Hello everyone,   I have a question regarding PDB deposition.   The processed diffraction data are in P6₃22, while the refined structure is in P6₃. During PDB deposition, the validation server reports a completeness of only ~51% which appears to result from the difference in symmetry between the processed data and the refined model.   Would it be acceptable to deposit the structure in this situation, or should the diffraction data be reprocessed in P6₃ and refined again before deposition?   Thank you very much for your advice! Best, Betul

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Re: phenixbb Digest, Vol 246, Issue 21 (out of office)
by Elisabeth Laurent 26 Jun '26

26 Jun '26

Thank you for your email. I am currently out of the office until July 1, 2026. I will respond to your email as soon as possible upon my return. For urgent matters, please contact: bmca(a)boku.ac.at Thank you for your understanding. Kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 26.6.26 23:41 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. CBMS Lecture Series - Chakraborty - 24 June 2026 (Stojanoff, Vivian) 2. DECTRIS assumes stewardship of XDS (Kay Diederichs) 3. Cryo-EM staff scientist opportunity in Madison, WI (Eric Montemayor) ---------------------------------------------------------------------- Message: 1 Date: Thu, 18 Jun 2026 23:54:22 +0000 From: "Stojanoff, Vivian" <stojanof(a)bnl.gov> Subject: [phenixbb] CBMS Lecture Series - Chakraborty - 24 June 2026 To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: "Stojanoff, Vivian" <stojanof(a)bnl.gov> Message-ID: <DM6PR09MB53509CC4CDC4BD3359082AA9CEE32(a)DM6PR09MB5350.nam prd09.prod.outlook.com> Content-Type: text/plain; charset="utf-8" You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Saumen Chakraborty The University of Mississippi WEDNESDAY, June 24, 13:30 (EDT) "Artificial Metalloproteins to Harvest Solar Energy and Small Molecule Activation" Register in advance for this meeting: https://bnl.zoomgov.com/j/1608968233?pwd=zJn5FYvcPM58P1CfantsS6bhTiMIIW.1 Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Metalloenzymes catalyze complex reactions with unprecedented efficiency. These enzymes are promising candidates for various biotechnological applications, including producing alternative fuels and pharmaceuticals. Oftentimes, the innate complexity of these metalloenzymes prohibits a true appreciation of their full capability and a detailed understanding of their structure-function relationships. One approach to alleviating this issue is to design artificial metalloenzymes (ArMs) that still contain the metal of interest in a biomolecular environment, allowing the chemistry to be performed in aqueous media. The protein scaffold prevents unwanted side reactions. In addition, the protein environment allows one to alter outer sphere interactions to fine-tune their reorganization energies and reactivity. In this seminar, I will present two complementary approaches to designing Ni and Cu-containing ArMs – artificial hydrogenases and artificial C-H peroxidation catalysts utilizing protein reengineering and de novo protein design approaches. ------------------------------ Message: 2 Date: Tue, 23 Jun 2026 08:24:37 -0000 From: "Kay Diederichs" <kay.diederichs(a)uni-konstanz.de> Subject: [phenixbb] DECTRIS assumes stewardship of XDS To: phenixbb(a)phenix-online.org Message-ID: <178220307724.3620199.8539268109861560581(a)cci3.lbl.gov> Content-Type: text/plain; charset="utf-8" DECTRIS, a major manufacturer of X-ray and electron detectors, has assumed official stewardship of XDS. As most readers of this mailing list used globally in macromolecular crystallography to process raw diffraction data. The software plays a critical role in helping structural biologists determine the 3D structures of complex biomolecules. By taking over its management, DECTRIS guarantees the long-term maintenance, stability, and compatibility of this scientific tool. A primary goal of the corporate stewardship is to ensure long-term availability, and scientific reproducibility of results. DECTRIS has committed to keeping XDS completely free of charge for academic and non-profit research use. DECTRIS is removing the 12-month expiration constraint that previously forced academics to update their software. There will be a single version of XDS for both academic and proprietary use, which will be publicly downloadable upon registration. Academic users will enjoy unlimited free use. Furthermore, academic labs and beamlines that process data on behalf of commercial customers holding a valid XDS license will not need to purchase a separate license themselves. The company's backing transitions a historically single-developer academic codebase into a secured, corporate-supported framework. However, Wolfgang Kabsch and I keep working on XDS. For more information, please read the official press release at https://dectris.com/en/company/news/newsroom/news/dectris-assumes-stewardsh… Kay Diederichs ------------------------------ Message: 3 Date: Fri, 26 Jun 2026 16:40:29 -0500 From: Eric Montemayor <montemayor.eric(a)gmail.com> Subject: [phenixbb] Cryo-EM staff scientist opportunity in Madison, WI To: phenixbb(a)phenix-online.org Message-ID: <CAL4G_aJMuc6JWwQHHBTL3BoVbSx75HgObedUWZ7b3ATwuizn3Q(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" See below if you’re interested in driving cutting-edge science and technology development at the interface of academia and industry! --------------------------------------------------- UW-Madison’s Department of Biochemistry currently has a full-time opening for a Cryo-EM Scientist in the Cryo-EM Research Center (CEMRC) and NIH-supported Midwest Center for Cryo-Electron Tomography (MCCET). These centers house state-of-the-art instrumentation and computational infrastructure, including multiple 300 keV and 200 keV TEMs, cryo-FIB-SEMs, along with conventional and high-pressure vitrification equipment. The centers provide hands-on training for all new staff so they are subsequently empowered to train and support users across the entire experimental and computational cryo-EM/ET workflow. The centers also provide their staff with opportunities for co-authoring publications, presenting at conferences, obtaining grant-writing experience, along with gaining experience in user-facing scientific support. Additional details linked below. Informal inquiries may be sent to cryoem(a)biochem.wisc.edu https://jobs.wisc.edu/jobs/cryo-em-scientist-madison-wisconsin-united-states https://cryoem.wisc.edu/ https://www.cryoetportal.org Regards, Eric J. Montemayor, PhD. ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org ------------------------------ End of phenixbb Digest, Vol 246, Issue 21 *****************************************

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Cryo-EM staff scientist opportunity in Madison, WI
by Eric Montemayor 26 Jun '26

26 Jun '26

See below if you’re interested in driving cutting-edge science and technology development at the interface of academia and industry! --------------------------------------------------- UW-Madison’s Department of Biochemistry currently has a full-time opening for a Cryo-EM Scientist in the Cryo-EM Research Center (CEMRC) and NIH-supported Midwest Center for Cryo-Electron Tomography (MCCET). These centers house state-of-the-art instrumentation and computational infrastructure, including multiple 300 keV and 200 keV TEMs, cryo-FIB-SEMs, along with conventional and high-pressure vitrification equipment. The centers provide hands-on training for all new staff so they are subsequently empowered to train and support users across the entire experimental and computational cryo-EM/ET workflow. The centers also provide their staff with opportunities for co-authoring publications, presenting at conferences, obtaining grant-writing experience, along with gaining experience in user-facing scientific support. Additional details linked below. Informal inquiries may be sent to cryoem(a)biochem.wisc.edu https://jobs.wisc.edu/jobs/cryo-em-scientist-madison-wisconsin-united-states https://cryoem.wisc.edu/ https://www.cryoetportal.org Regards, Eric J. Montemayor, PhD.

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DECTRIS assumes stewardship of XDS
by Kay Diederichs 23 Jun '26

23 Jun '26

DECTRIS, a major manufacturer of X-ray and electron detectors, has assumed official stewardship of XDS. As most readers of this mailing list know, XDS is a software package used globally in macromolecular crystallography to process raw diffraction data. The software plays a critical role in helping structural biologists determine the 3D structures of complex biomolecules. By taking over its management, DECTRIS guarantees the long-term maintenance, stability, and compatibility of this scientific tool. A primary goal of the corporate stewardship is to ensure long-term availability, and scientific reproducibility of results. DECTRIS has committed to keeping XDS completely free of charge for academic and non-profit research use. DECTRIS is removing the 12-month expiration constraint that previously forced academics to update their software. There will be a single version of XDS for both academic and proprietary use, which will be publicly downloadable upon registration. Academic users will enjoy unlimited free use. Furthermore, academic labs and beamlines that process data on behalf of commercial customers holding a valid XDS license will not need to purchase a separate license themselves. The company's backing transitions a historically single-developer academic codebase into a secured, corporate-supported framework. However, Wolfgang Kabsch and I keep working on XDS. For more information, please read the official press release at https://dectris.com/en/company/news/newsroom/news/dectris-assumes-stewardsh… Kay Diederichs

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CBMS Lecture Series - Chakraborty - 24 June 2026
by Stojanoff, Vivian 18 Jun '26

18 Jun '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Saumen Chakraborty The University of Mississippi WEDNESDAY, June 24, 13:30 (EDT) "Artificial Metalloproteins to Harvest Solar Energy and Small Molecule Activation" Register in advance for this meeting: https://bnl.zoomgov.com/j/1608968233?pwd=zJn5FYvcPM58P1CfantsS6bhTiMIIW.1 Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Metalloenzymes catalyze complex reactions with unprecedented efficiency. These enzymes are promising candidates for various biotechnological applications, including producing alternative fuels and pharmaceuticals. Oftentimes, the innate complexity of these metalloenzymes prohibits a true appreciation of their full capability and a detailed understanding of their structure-function relationships. One approach to alleviating this issue is to design artificial metalloenzymes (ArMs) that still contain the metal of interest in a biomolecular environment, allowing the chemistry to be performed in aqueous media. The protein scaffold prevents unwanted side reactions. In addition, the protein environment allows one to alter outer sphere interactions to fine-tune their reorganization energies and reactivity. In this seminar, I will present two complementary approaches to designing Ni and Cu-containing ArMs – artificial hydrogenases and artificial C-H peroxidation catalysts utilizing protein reengineering and de novo protein design approaches.

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