- phenixbb - phenix-online.org

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

Large project database = slow opening of Phenix GUI?
by Harry Mark Greenblatt 26 Apr '26

26 Apr '26

BS”D Hi all, Has anybody experienced slow opening of the Phenix GUI, when a person has amassed well over a decade worth of projects, or should that not affect the startup speed? Thanks Harry -------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Chemical and Structural Biology harry.greenblatt(a)weizmann.ac.il<mailto:[email protected]> Weizmann Institute of Science Phone: 972-8-934-6340 234 Herzl St. Facsimile: 972-8-934-3361 Rehovot, 7610001 Israel

1 0

Unable to open phenix.refine
by p.r.tiley＠pgr.reading.ac.uk 20 Apr '26

20 Apr '26

Has anyone had problems trying to open phenix.refine? I have installed Phenix 2.0.5936 several times but keep on getting the following error message when I click on phenix.refine: KeyError : 'Unrecognized input file parameter refinement.gui.migration.refinement.input.sequence.file_name (allowed: data_manager.model.file, refinement.reference_model.file, refinement.gui.migration.refinement.input.pdb.file_name, refinement.gui.migration.refinement.input.pdb.neutron_file_name, refinement.gui.migration.refinement.input.pdb.electron_file_name, refinement.den.reference_file).' Any help/advice would be much appreciated. Thanks in anticipation!

4 5

Buy popular peptides (WHSAP +49 1521 2578535)
by cory84522＠gmail.com 09 Apr '26

09 Apr '26

Spring deals are here! Enjoy exclusive discounts on a wide range of popular peptides — while supplies last ⏳ 💎 Full Price List RT10mg – $80 RT20mg – $155 RT30mg – $189 RT40mg – $245 RT50mg – $299 RT60mg – $355 T15mg – $59 T25mg – $70 BPC 10mg – $58 BPC 20mg – $109 TB 5mg – $70 Mots-c 5mg – $40 Tesa 5mg – $75 CJC 10mg – $135 Semax 5mg – $40 Selank 5mg – $39 IPA 10mg – $65 IPA 20mg – $125 DSIP 10mg – $65 VIP 10mg – $140 Oxy 10mg – $69 EPI 10mg – $65 EPI 50mg – $219 TA-1 10mg – $159 GHKCU 100mg – $79 NAD+ 1000 – $129 THY-10mg – $65 CJC + IPA (10/10) 20mg – $189 KPV 30mg – $199 💥 Special Offer 🛒 FREE Shipping on orders over $350 (including bac water) 📦 Orders under $350: flat $20 shipping fee 📩 How to Order Send us the following details: Product(s) Your Name Phone Number Shipping Address (City, State, ZIP Code, Country) Email 💰 Payment Methods BTC | USDT (TRON / Ethereum / Solana) USDC (Ethereum / Solana) | PYUSD 📲 Contact Dr Harry ❤️ 📧 Email: cory84522(a)gmail.com 📱 WhatsApp: +49 1521 2578535 Telegram: @Medline_pharma

1 0

Re: coot-1 linked to phenix
by Roberto Steiner 06 Apr '26

06 Apr '26

Hi Chiara I have installed coot-1 using homebrew and using /opt/homebrew/Cellar/coot/1.1.20/bin/coot works for me. Ciao Roberto Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours. On 28/01/2026, 13:27, "Rapisarda, Chiara /FR via phenixbb" <phenixbb(a)phenix-online.org <mailto:[email protected]>> wrote: Hello, I have a Mac that I upgraded to Tahoe, and now coot 0.9 isn’t working any more. I would like to link phenix to coot-1. I can do that by adding: /Applications/ccp4-9/coot_py3/bin/coot To the coot path in preferences, but after a refinement when I open coot , it is open but it is not connected to the phenix refine job and no PDB nor map is open. I am aware that I can manually open the map and pdf, I would like to know if coot-1 can be opened in a way that will allow me to navigate the structure using phenix. When I ask gemini it tells me that I should point it to: /Applications/ccp4-9/bin/coot-py3 But it doesn’t exist in my ccp4 installation. Has anyone successfully managed to link coot-1 to phenix using a good bridge? Any help will be greatly appreciated. Best, Chiara _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org <mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org <mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

3 3

ReadySet and cif
by p.auffinger＠unistra.fr 02 Apr '26

02 Apr '26

Hi, Is it possible to get a cif file as an output when using the ReadySet gui ? What is "Output file base" ? If I precise "output.cif" the program seems not to be happy ! Thanks, Pascal

4 3