- phenixbb - phenix-online.org

working with composite models
by Dmitry Semchonok 06 Jun '26

06 Jun '26

Dear Colleagues, We're encountering an issue with composite model refinement and would appreciate your advice. Our scenario: 1. We built two separate models based on two subtracted maps of a single complex. 2. We have a lower-resolution map of the full complex. 3. We merged the two models into the full complex and refined it against the full map. The problem: When refining the merged model against the full map using real-space refinement in Phenix, the clashscore progressively worsens. Has anyone experienced similar issues, or can you offer suggestions on addressing this problem? Thank you for your insights. Best regards, Dmitry

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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 06 Jun '26

06 Jun '26

Hi Andrea, in your case, phenix.refine seems to fill bulk solvent into volumes that are not actually filled by solvent. It might help to optimize the mask, see https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… "6. Mask parameters". Best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Re: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 06 Jun '26

06 Jun '26

Just a reminder that registration is open for the CCP4 Study Weekend taking place in January 2025. Early bird deadline is 11 November so if you want to save some money or are a student wanting a standard bursary register ASAP. Applications for Travel bursaries are now open but close at the end of the month so get your applications in now! Hope to see you there!! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK) From: McIntyre, Karen (STFC,RAL,SC) Sent: 26 September 2024 13:15 To: CCP4 WG2 <ccp4wg2(a)listserv.stfc.ac.uk>; CCP4 WG1 <ccp4wg1(a)listserv.stfc.ac.uk>; ccp4bb(a)jiscmail.ac.uk Subject: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models Importance: High Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK)

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PostDoc position in time resolved serial crystallography at ESRF ID29 beamline
by Daniele de Sanctis 06 Jun '26

06 Jun '26

Dear all, We have an exciting opportunity for a Post Doc position at the new ID29 serial crystallography beamline at the ESRF. Cheers Daniele The ID29 beamline is the first serial crystallography beamline for room temperature, time-resolved studies at a high energy 4th generation synchrotron. It delivers an unmatched flux density, enabling diffraction data collection from micro-sized samples in a few microseconds, allowing exploration of structural changes at room temperature. The beamline features state-of-the-art equipment, with fast goniometer for fixed target and liquid sample delivery, a high dynamic range integrating detector and laser probes. A dedicated sample preparation laboratory supports crystal delivery systems like injectors, fixed targets and microfluidic devices. You will focus on developing novel environments for crystal handling and delivery systems for serial crystallography experiments, as well as novel data collection methods and applying them to study time-resolved enzymatic reactions in crystals. You will also participate in beamline operations, support external users as the local contact, and have the opportunity to develop your own research and collaborations. Further information please contact Daniele de Sanctis (tel.: +33 (0)4 76 88 28 69, email: daniele.de_sanctis(a)esrf.fr <XXX(a)esrf.fr>). Applications should be submitted through the ESRF portal https://esrf.gestmax.eu/1816/1/post-doc-on-id29/en_US Expected profile - PhD in chemistry, physics, biophysics, biology or closely related science obtained less than 3 years ago - A strong background in X-ray crystallography and serial crystallography is desirable - A strong interest in new method development - Ability to interact with multi-disciplinary staff and facility users - English proficiency (working language at the ESRF) Working conditions The salary will be calculated on the basis of relevant qualifications and professional experience. Do you recognize yourself in this description? Apply now for your next professional adventure! What we offer: 1. *Join* an innovative international research institute, with a workforce from 38 different countries 2. *Collaborate* with global experts to advance science and address societal challenges 3. Come and live in a *vibrant city*, in the heart of the Alps, and Europe's Green Capital 2022 4. *Enjoy* a workplace designed to support your *quality of life* 5. Benefit from our* competitive compensation* and *allowances* *package*, including *financial support for your relocation to Grenoble* For further information on employment terms and conditions, please refer to https://www.esrf.fr/home/Jobs/what-we-offer.html The ESRF is an equal opportunity employer and encourages applications from disabled persons.

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Polder map
by jirivitali＠gmail.com 06 Jun '26

06 Jun '26

Dear Phenix user I wanted to create Polder map. I just used single atom or residues and it works fine. There is also a option for the compute box but I am more interested to create map by selecting more than one resides but without using the compute box. Is it possible? and what will be the syntax for this. best J. Vitali

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Phenix error in real space refinement with ligand
by Yung-Chieh Chen 06 Jun '26

06 Jun '26

Dear all, I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance. Best wishes, Yung-Chieh Chen

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cryo em map
by iram aziz 06 Jun '26

06 Jun '26

Hello All. I got a nice 2.45 Angstrom map from cryo em data. I checked handedness, map model fitting on the chimera and opened in the coot. It looks nice. Can you please give me suggestions about the Phenix refinement steps. Thanks Iram

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Handling of modified nucleotides in ribosome structures
by christian.steinmetzger＠imbim.uu.se 06 Jun '26

06 Jun '26

Dear community, I'm trying to work with a published ribosome structure (PDB 7K00, https://www.rcsb.org/structure/7k00 ) for example in phenix.combine_focused_maps or phenix.real_space_refine. Of course this structure contains a lot of modified residues and the monomer library in a fresh Phenix installation (version 1.21.2-5419) does not handle these out of the box. Since a lot of publications have used 7K00 as a starting point for their work in Phenix and since the current CCP4 monomer library plays nice with this structure I would not have expected this. Am I missing something in my Phenix setup to make it recognize such "common" modified residues in a ribosome or do I indeed need to generate parameters myself using AceDRG, eLBOW, Grade2 etc.? In the latter case, could I simply swap out the stock Phenix monomer library for the one from CCP4 as a drop-in replacement or would that be a bad idea? Thank you! Christian

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26th West Coast Structural Biology Workshop - March 23-26, 2025 @ Asilomar Conference Center
by Michael Thompson 06 Jun '26

06 Jun '26

Dear Colleagues, Happy New Year!! We are writing to share information about the upcoming West Coast Structural Biology Workshop, which is scheduled for March 23-26, 2025 at its traditional location, the picturesque Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions focusing on the contributions of students and postdocs. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). Please note that the registration deadline is Feb. 7, 2025. We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is January 20, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Error phenix refine with ligands
by miriam.cavinato＠unimi.it 06 Jun '26

06 Jun '26

Hi everyone, I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance Best regards Miriam

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