- phenixbb - phenix-online.org

comprehensive validation (cryoem)
by Roberto Marabini 05 Jun '26

05 Jun '26

Hi, We are using the Phenix protocol "Comprehensive Validation (CryoEM)" (version 2.0.5936). The input structure file is provided in mmCIF format. We have observed that the protocol fails when chain IDs contain three characters, whereas it completes successfully when chain IDs contain two characters. Based on this behavior, we suspect that the protocol may internally convert the input mmCIF file to the legacy PDB format. Could you please confirm whether this assumption is correct? If such a conversion is performed internally, we would also like to understand how the protocol handles structures that exceed the limitations of the PDB format, for example files containing more than 99,999 atoms or chain identifiers that are not supported by the traditional PDB specification. When the protocol fails the following warnings are reported: Bad HELIX record, was skipped: HELIX 1 1 MET0Ah 7 HIS0Ah 14 1 8 Bad HELIX record, was skipped: HELIX 2 2 SER0Ah 25 GLU0Ah 36 1 12 ... Bad sense in SHEET record: '9' Thank you for your help. Best regards, Roberto

2 2

Phenix 2.1-6048 macOS / REEL (eLBOW) stability issue
by Xavier Brazzolotto 04 Jun '26

04 Jun '26

Hi, Phenix users and developers Using the recent Phenix release (2.1.6048), I am experiencing stability issues when inspecting eLBOW results in the REEL interface. The REEL interface systematically closes after some manipulations, crashing the whole Phenix interface. Are any users also impacted? I am using a Phenix on a MacBook Pro M2 (Apple Silicon) Xavier

1 0

Seeking Advice on Difficult MR Case: TFZ 6–8 for All Search Models, R-free ~0.50
by syedsuhail7654＠gmail.com 03 Jun '26

03 Jun '26

I am working on a protein containing two domains: an N-terminal FHA domain and a C-terminal RING domain. I have collected a native dataset that extends to 2.45 Å resolution in space group P2₁2₁2 with unit-cell parameters approximately a = 46.9 Å, b = 91.9 Å, c = 165.0 Å. I have been struggling to obtain a convincing molecular replacement solution despite trying multiple approaches. What I have tried so far: Full-length AlphaFold model as a search model. Splitting the AlphaFold model into individual FHA and RING domains. Sequential/domain-wise MR searches. Aggressive model trimming. Poly-alanine versions of the models. Various combinations of domain placement strategies. However, the results remain largely the same: TFZ values are consistently in the range of 6–8. LLG values are not particularly convincing. Refinement of the best solutions leads to R-free values around 0.50 or higher. Electron-density maps are not readily interpretable. No solution has shown clear evidence of being correct after refinement and map inspection. At this stage I am trying to determine whether the issue is: Failure of MR due to domain rearrangement between the FHA and RING domains. Incorrect number of molecules in the asymmetric unit. Partial placement of domains that is being missed. Crystal pathologies such as pseudo-symmetry or translational NCS. Some other issue that I may be overlooking. I would appreciate suggestions on: Additional diagnostics to assess whether any of these TFZ 6–8 solutions might actually be correct. Strategies for multi-domain MR in cases where AlphaFold-based models are unsuccessful. Whether further model editing is likely to help. Other MR pipelines that may be worth trying before moving to experimental phasing. Any advice would be greatly appreciated.

8 9

Macromolecular Crystallography - CSHL Course October 2026
by Paul Adams 19 May '26

19 May '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). 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: July 17 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 ] --

1 0

hydrogens.refine = individual *riding
by p.auffinger＠unistra.fr 16 May '26

16 May '26

Hi, Can these options be used with real_space refinement - hydrogens.refine = individual *riding - hydrogens.refine_occupancie Thanks, Pascal

1 0

Phenix version 2.1 released
by Paul Adams 06 May '26

06 May '26

Dear Colleagues, The Phenix developers are excited to announce that version 2.1 of Phenix is now available (build 2.1-6048). Binary installers for Linux, Mac OSX, and Windows, and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this new version of Phenix include: - Phenix AI agent available in GUI - Add integration with Coot 1 - Fix integration with PyMOL - Fix bug with reading 16-bit float MRC maps (mode 12) This publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix has previously been funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is currently funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) 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 ] --

1 0

CBMS Lecture Series - Callero - May 6, 2026; 13:30 (EDT)
by Stojanoff, Vivian 01 May '26

01 May '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Guillermo Calero, MD PhD University of Pittsburgh School of Medicine WEDNESDAY, May 6, 13:30 (EDT) "Fine-tuning Time Resolved Experiments to Capture Crystal Biochemistry" Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/TztZw5fpSr-kBHygBEuzwA Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Typically, interactions between enzymes and substrates (or inhibitors), are viewed in terms of small molecules binding to relatively rigid proteins. However, computational and experimental studies demonstrate that proteins undergo a variety of molecular motions over a wide range of timescales. Such conformational flexibility is integral to enzyme activity, drug action and drug resistance. Contemporary structural biology approaches resolve only the structures of thermodynamically stable species. By contrast, time resolved (TR) structural studies using crystallography or single particle cryoEM are innovative tools that reveals details of both the ligand binding process and the stepwise chemistry of the reaction, with important biomedical applications. Through a combination of TR techniques, including UV photolysis of caged substrates, we have used TR techniques to create the first molecular movies of: 1) b-lactam antibiotics binding to b-lactamases; 2) deoxynucleotide addition by HIV-1 Reverse Transcriptase (RT); 3) nucleotide addition by RNA polymerase II (Pol II); and 4) GTP hydrolysis by N-RAS. =================================== 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

1 0

real space refinement with a reference model
by Valérie Biou 29 Apr '26

29 Apr '26

Dear all, I would like to use a reference model to try to improve my cryo-em refinement geometry. I have an AF3 model that superposes with an RMSD of 1.4Å wrt my structure, and I renumbered the residues so they match with my structure. however, I get the message Reference Model Matching Summary: reference file: renumbered.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0 input file list (truncated from the root) default_model = "RealSpaceRefine_72/rsr71_isolde1_real_space_refined_072.pdb" real_map_files = /cryosparc_P29_J343_010_volume_map_sharp.mrc" default_real_map = cryosparc_P29_J343_010_volume_map_sharp.mrc" restraint_files = eLBOW_46/elbow.P.P_pdb.001.cif" default_restraint = eLBOW_46/elbow.P.P_pdb.001.cif" phil_files = Phenix/.phenix/project_data/real_space_refine_88.eff" default_phil = Phenix/.phenix/project_data/real_space_refine_88.eff" then : reference_model { enabled = True file = "renumbered.pdb" side_chain = False secondary_structure_only = True search_options { chain_max_rmsd = 3.0 Can you please help me with this? Kind regards Valérie

2 1

refining HO2' atoms
by p.auffinger＠unistra.fr 29 Apr '26

29 Apr '26

Hi all, Is there an easy way to only refine hydroxyl atoms (like ribose HO2' atoms) in Phenix.refine ? I understand that it can be done in readySet. Thanks, Pascal

1 1

Riding hydrogens
by p.auffinger＠unistra.fr 27 Apr '26

27 Apr '26

Dear all, I am trying to refine a high-resolution cryo-EM structure. However, some of the guanine NH2 groups end up out of plane (I used cdl). Is that an expected behavior ? It seems that may be planarity restraints associated with hydrogens are not strong enough. Is there an option to augment them ? May be also the riding option only involves distance and angle restraints ? This is not clear from the manual to me. Also, for OH groups like ribose 2'-OH groups, I assume that the riding option only involves distance restraints and that these H-atoms are otherwise free to rotate Can you please help me out here ? Thanks, Pascal

4 3