- phenixbb - phenix-online.org

atom selection for elements anisotropic rest TLS
by Georg Mlynek 10 Sep '25

10 Sep '25

Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg.

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help with circular peptide cif file creation
by John Bruning 07 Sep '25

07 Sep '25

Dear Phenix BB, We have a 15 aa circular peptide. It has numerous non-natural amino acids, including 1-2 that aren't in the PDB anywhere. Where have created a cif file that allows Phenix refine to run without craching, but I am not sure I am doing it right, and it was kind of complicated. I was wondering if there was anyone out there with ample experience with this type of thing that could help us check over our cif and more importantly recommend the best way to make these cif files in the future. Thanks, Dr. John B. Bruning Head, Laboratory of Protein Crystallography and Structural Biology Associate Professor Oracle For Research Fellow Institute of Photonics and Advanced Sensing School of Biological Sciences, Discipline of Molecular and Biomedical Science Faculty of Sciences, Engineering and Technology The University of Adelaide Adelaide, South Australia 5005 Telephone: +61 08 8313 5218 Email address: john.bruning(a)adelaide.edu.au<mailto:[email protected]>

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Postdoctoral Position – Computational Methods for Cryo-EM at LBNL
by Pavel Afonine 03 Sep '25

03 Sep '25

Dear community, Posting on behalf of Kanupriya Pande: I’d like to draw your attention to the following job opening at Lawrence Berkeley National Laboratory (California, USA): We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project on computational methods development for cryo-electron microscopy. The project is on developing mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with preferred orientation, incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building aspects. The position can start as early as Oct 1, 2025. Full details of the position and job requirements can be found here: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Please feel free to share this opportunity with anyone who might be interested. Kind regards, Pavel

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partial structure refinement
by James Holton 02 Sep '25

02 Sep '25

Greetings PhenixBB, I have a question that keeps coming up again and again. If I have a part of my structure that is a blob of density and I have a map of what that density cloud looks like, is there any way in phenix to include that blob as part of the refinement? Perhaps giving it its own scale and B factor? One example might be a user-defined bulk solvent map, but a disordered ligand or domain can also come up. Traditionally, in older refinement programs this was called a "partial structure", and it is a feature still supported in refmac5. You give it "FPART=F PHIP=P" in the input mtz file. Last I checked there was no way to do this in phenix. Is that still true? Any recommended ways to do things like this? Thanks for your help and insight, -James Holton MAD Scientist

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Pittsburgh Diffraction Conference 2025 - Pre Conference Workshop - Last Days to register
by Stojanoff, Vivian 26 Aug '25

26 Aug '25

Pittsburgh Diffraction Conference You are cordially invited to attend the Pre-Conference Workshop, Crystal Clear Insights: Mastering Protein Crystallization (for the future) LAST DAYS for REGISTRATION AUGUST 29, (Friday 2025 This hands-on workshop will be held at NSLS II on October 9 prior to the Pittsburgh Diffraction Conference. “Crystal Clear Insights” introduces crystallizations methods for the upcoming X-ray sources (time resolved, room temperature, serial crystallography), electron microscopy and neutron diffraction. REGISTRATION by August 29, 2025, in the Brookhaven National Laboratory Guest, User and Visitor Center (GUV), if you do not have a valid BNL Guest appointment. To register follow instructions: https://guest.bnl.gov/ Contact: Vivian Stojanoff by email (stojanof(a)bnl.gov) and use “PDC 2025 – Crystal Clear” for your subject line Program: Lecture: From Gene to Crystallization Crissy Tarver, SLAC Hand-on Topics: Exploring the Phase Diagram for crystals for all applications Patrick Stewart, Douglas Instruments Ltd. Nanoliter and nano/micro sized crystals using the Acoustic Droplet Ejector Alex Soares, NSLS II Microfluidics crystallization and X-ray Diffraction Sarah Perry, UMASS Amherst Vapor Diffusion Methods Darya Marchany-Rivera, SSRL Sample prep for electron microscopy and X-ray diffraction Joyce Frank (Mitegen) & Crissy Tarver (SLAC)

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CBMS invites - PDC2025 workshop Crystal Clear Insights - Deadline August 29
by Stojanoff, Vivian 22 Aug '25

22 Aug '25

The Center for Biomolecular Structure invites you to participate in the 82th Pittsburgh Diffraction Conference (PDC) PDC 2025 - Pre Conference hands-on workshop: Crystal Clear Insights: Mastering Protein Crystallization registration deadline AUGUST 29. This workshop guides you through cutting-edge crystallization strategies tailored to X-ray, electron, or neutron diffraction. You will explore the latest approaches for producing microcrystals for serial experiments, designing crystallization pipelines for fragment screening, optimizing conditions for time-resolved crystallography. Alongside the core methods, we’ll highlight practical tips and tricks drawn from current practice: from seeding strategies and microcrystal preparation to cryoprotection, and sample delivery. To register please follow instructions provided: https://www.bnl.gov/pittsburgh-diffraction-conference/reg/step1.php ALL participants need to register as well in the Guest, User and Visitor Center as this workshop will take place at the National Synchrotron Light Source II https://guest.bnl.gov/ ON THE PROGRAM : Lecture: From genes to structure - Crissy Tarver (SLAC) Hands-on * Learn tricks and tips: from hanging drops to sitting drops in vapor diffusion methods Darya Marchany-Rivera (SLAC) * Explore the Phase Diagram for crystals for all applications ; Patrick Shaw Stewart (Douglas Instruments Ltd.) * Learn about nanoliter and nano/micro-sized crystals using the Acoustic Dropplet Ejector; Alex Soares (NSLS II) * Discover microfluidics crystallization and X-ray diffraction; Sarah Perry (University of Massachusetts Amherst) * From crystals to cryo EM samples: what they have in common; Joyce Frank (Mitegen LLC) & Crissy Tarver (SLAC) For accommodations we suggest HomeSuites2by Hilton Long Island Brookhaven (https://www.hilton.com/en/locations/usa/new-york/yaphank/home2-suites/), and Springhill Suites by Marriott Long Island Brookhaven (https://www.marriott.com/en-us/hotels/ispsh-springhill-suites-long-island-b…) ask for discount for longer stay.

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Pacific Northwest CryoEM Center Modelling Workshop
by Davulcu, Omar 21 Aug '25

21 Aug '25

Dear all, The Pacific Northwest CryoEM Center is excited to announce that registration is open for our first Atomic Modelling and Validation in CryoEM workshop! This virtual workshop is open to all and will explore current methods, best practices, and potential pitfalls of atomic modelling in cryoEM. Join us on September 3 - 5 to hear software developers and end users discuss state-of-the-art modelling tools and their applications. Registration is required and free and open to all. Please see the attached flyer to learn more and visit http://tinyurl.com/Cryo-EMModeling to register! Best, Omar Davulcu Scientific Point of Contact Pacific Northwest Cryo-EM Center http://pncc.labworks.org<http://pncc.labworks.org/>

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Reminder: CBMS Lecture Series - daSilva - August 20, 13:30 (EDT)
by Stojanoff, Vivian 19 Aug '25

19 Aug '25

You and your co-workers are cordially invited to join us ..... "AI Tools in X-ray Computed Tomography: Applications, Drawbacks, and Key Insights." Julio-Cesar da Silva CNRS NÉEL Institute Grenoble, France August 20, 13:30(EDT) To register for virtual attendance: https://bnl.zoomgov.com/meeting/register/haKdzCvnReWMVziXnFXMZw Abstract: I will present the most commonly used AI tools in X-ray computed tomography, highlighting their potential drawbacks. Moreover, I will discuss the basic machine learning concepts essential for effectively utilizing these tools and their implementation at the Hub AI for Tomography, AIAX, located in Grenoble, France. After examining densely connected neural networks, convolutional neural networks, and encoder-decoder architectures, I will provide a brief explanation of how the U-Net, MSDNet, Noise2Noise, TomoGAN, and GANRec networks function within the field of tomography. Their primary applications focus on image denoising and 3D image segmentation. The examples provided will be sourced from hard X-ray tomography applied to both biological and materials science specimens. The key takeaway from this presentation is that while AI-generated results can be advantageous, they need to be critically evaluated, as they always require human involvement for refinement. ================= 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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PDC 2025 > PRE-Conference: Pittsburgh Diffraction Conference - registration deadline August 25,2025
by Stojanoff, Vivian 14 Aug '25

14 Aug '25

Pittsburgh Diffraction Conference You are cordially invited to attend the Pre-Conference Workshop, Crystal Clear Insights: Mastering Protein Crystallization This hands-on workshop will be held at NSLS II on October 9 prior to the Pittsburgh Diffraction Conference. “Crystal Clear Insights” aims to discuss basic and advance protein crystallization methods for advanced structural diffraction data collection. Participants will be able to select three of the five parallel hands-on sessions. To register: https://www.bnl.gov/pittsburgh-diffraction-conference/index.php If you want to register only for the workshop contact Vivian Stojanoff by email (stojanof(a)bnl.gov) and use “PDC 2025 – Crystal Clear” for your subject line. Participation is limited to 20 participants; those who wish to attend only the pre-Conference workshop will be placed on a waiting list and informed by August 26, 2025. ALL “Crystal Clear” pre-Conference PARTICIPANTS need to register until August 25, 2025, in the Brookhaven National Laboratory Guest, User and Visitor Center (GUV), as well, if you do not have a BNL Guest appointment. To register follow instructions: https://guest.bnl.gov/ If you have any question, contact: stojanof(a)bnl.gov. Tentative Program: Lecture: From Gene to Crystallization Crissy Tarver, SLAC Hand-on Topics: Vapor Diffusion Methods - from hanging drops to sitting drops Darya Marchany-Rivera, SSRL Exploring the Phase Diagram for crystals for all applications Patrick Stewart, Douglas Instruments Ltd. Nanoliter and nano/micro sized crystals using the Acoustic Droplet Ejector Alex Soares, NSLS II Microfluidics crystallization and X-ray Diffraction Sarah Perry, UMASS Amherst Sample prep for electron microscopy and X-ray diffraction TBD All topics will be offered in parallel, participants will be able to choose 3 topics and rotate through them.

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Inquiry on RMS Value in Phenix PredictAndBuild MR Output
by zx2020＠connect.hku.hk 11 Aug '25

11 Aug '25

Dear All, I hope this email finds you well. While reviewing the MR-related output files generated by Phenix PredictAndBuild (see attached screenshot), I noticed that an RMS value is set in the Phaser input section. I found that in certain cases this parameter can have a significant impact on MR results. Could you kindly advise how this RMS value is determined or calculated within Phenix PredictAndBuild? [??????] Thank you very much for your time and guidance. Best regards, Xin Zhang School of Biomedical Sciences, The University of Hong Kong

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Refine pixel size for EM map?
by Oliver Clarke 01 Aug '25

01 Aug '25

Hi, I remember asking about this some time ago, but I am not sure if it was ever implemented. Is there a way to refine just pixel size for an EM map in phenix.real_space refine (or another phenix utility)? Even just automatically rigid-body fitting a crystal structure and calculating the pixel size with max correlation would be handy. We do this at the moment using Chimera/ChimeraX, but an automated way to do it in phenix would be handy. In the absence of a crystal structure, I wonder if directly refining pixel size during real space refinement would be possible/reasonable at higher resolution (<2Å)? Cheers Oli

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Phenix LigandFit RSCC calculation questions
by Theo Teng 29 Jul '25

29 Jul '25

Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from LigandFit to other ligand placement methods, and your response would be appreciated. Best regards, -- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy

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Re: phenixbb Digest, Vol 235, Issue 4 (out of office)
by Elisabeth Laurent 29 Jul '25

29 Jul '25

Thank you for your e-mail. I am out of office until August 26th, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 29.7.25 20:38 >>> 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. Re: Structure with high clashscore (sazanov(a)ist.ac.at) 2. Re: Structure with high clashscore (Pavel Afonine) 3. Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 (Paul Adams) 4. Phenix LigandFit RSCC calculation questions (Theo Teng) 5. Re: Phenix LigandFit RSCC calculation questions (Bernhard Rupp) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2025 15:09:07 -0000 From: sazanov(a)ist.ac.at Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org Message-ID: <175319694772.2856041.9789770720208691588(a)cci3.lbl.gov> Content-Type: text/plain; charset="utf-8" Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). Best Leonid JEROME JOHNSON wrote: > Hello all, > > I'm happy to join the forum! I have a problem with clashscores and would be > grateful for support. > > I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved > to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand > commonly results in high clashscore values) and after numerous rounds of > refinement, the clashscore remains high at 11. I recently tried using > gromacs to energy minimize and got values of 5 and 3 (according to > molprobity), but after refinement these values immediately jumped back up > to ~30. > > I wondered if you could describe the best way to reduce these? > > Attached is my latest round of refinement should you wish to take a look! > > Best, > Jerome ------------------------------ Message: 2 Date: Tue, 22 Jul 2025 10:29:20 -0500 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org, jjohnson19(a)ku.edu.tr Message-ID: <b4b4a347-1f89-44a4-b61b-dac1d2344d24(a)lbl.gov> Content-Type: text/plain; charset=UTF-8; format=flowed Hi All, > Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). this is an interesting observation. MolProbity always adds all H to compute clashscore -- one can't compute clashscore without H present. I suspect having H on ligands only triggers it to 'think' that H are already present, and it computes clashscore without adding H to everything else. Could you please send me the file off list (the one that has H only on the ligand)? I think we better investigate this.. >> I'm happy to join the forum! I have a problem with clashscores and would be >> grateful for support. >> >> I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved >> to 2.7 Angstroms. For MD, >> commonly results in high clashscore values) and after numerous rounds of >> refinement, the clashscore remains high at 11. 11 looks just fine. Note, clashscore=0 is not the goal because clashscore does not account for non-standard links and for example, can count as a severe clash atoms involved into nonstandard links, and similar. In Phenix Comprehensive Validation, go over the table of clashes, they are sorted, worst first, and check and try to address top few worst offenders. Pavel ------------------------------ Message: 3 Date: Tue, 22 Jul 2025 10:52:38 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <616BD923-8C42-4BFA-BCAF-4B7E60F4AC9C(a)lbl.gov> Content-Type: text/plain; charset=utf-8 Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th 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 this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most 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 -- 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) 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 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 ] -- ------------------------------ Message: 4 Date: Tue, 29 Jul 2025 14:34:52 -0400 From: Theo Teng <theodoreteng(a)college.harvard.edu> Subject: [phenixbb] Phenix LigandFit RSCC calculation questions To: phenixbb(a)phenix-online.org Message-ID: <CAE39kgR2K4FxFye6YJKO9uWnwQECYhg2+AB=_vRb=NLkw9ToXA(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from Lig-- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy ------------------------------ Message: 5 Date: Tue, 29 Jul 2025 11:38:27 -0700 From: Bernhard Rupp <br(a)hofkristallamt.org> Subject: [phenixbb] Re: Phenix LigandFit RSCC calculation questions To: Theo Teng <theodoreteng(a)college.harvard.edu> Cc: phenixbb(a)phenix-online.org Message-ID: <CAA3s99dcrE3j8VRJ6cH__7jv9y1a-ve2sxWcRws3UtsKsUdmag(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" There is a modified quote from a famous statistician, which one might keep in mind on such ventures: All ligands are wrong, but some are useful. Cheers, BR ------------------------------------------------------ Bernhard Rupp https://www.hofkristallamt.org/ br(a)hofkristallamt.org br(a)ruppweb.org +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ People can be divided into three classes: The few who make things happen; The many who watch what is happening; and the overwhelming majority who have no clue what is happening. ------------------------------------------------------ On Tue, Jul 29, 2025 at 11:35 AM Theo Teng <theodoreteng(a)college.harvard.edu> wrote: > Dear Phenix developers, > > I hope this message finds you well. > > We had two specific questions about how the real-space correlation > coefficient (RSCC) is computed when using Phenix.LigandFit: > > 1. What radius is used around the ligand or search center when calculating > the RSCC during ligand fitting? Is this radius fixed or adaptive? > > 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? > > We aim to compare the placements from LigandFit to other ligand placement > methods, and your response would be appreciated. > > Best regards, > -- > > *Theodore W. Teng* > Harvard College | Class of 2027 > A.B. student in Chemical and Physical Biology > Secondary in Global Health and Health Policy > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > ------------------------------ 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 235, Issue 4 ****************************************

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Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 22 Jul '25

22 Jul '25

Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th 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 this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most 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 -- 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) 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 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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Structure with high clashscore
by JEROME JOHNSON 22 Jul '25

22 Jul '25

Hello all, I'm happy to join the forum! I have a problem with clashscores and would be grateful for support. I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30. I wondered if you could describe the best way to reduce these? Attached is my latest round of refinement should you wish to take a look! Best, Jerome

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Syntax help: phenix.pdb_tools to remove selected bases from file
by Vorländer,Matthias Kopano 21 Jul '25

21 Jul '25

Hi everyone, I am trying to truncate an RNA chain to backbone only using phenix.pdb tools with this command: phenix.pdbtools input.cif remove="(chain IN and not (phosphate or ribose)" I get: AtomSelectionError: RuntimeError: Atom selection syntax error at word "phosphate". Atom selection string leading to error: (chain IN and not (phosphate or ribose) Based on https://phenix-online.org/documentation/reference/atom_selections.html<https://phenix-online.org/documentation/reference/atom_selections.htmlI> I thought “phosphate” and “ribose” should be valid selection key words, but can’t figure out what I am doing wrong and would appreciate your help : ) Thanks in advance and best wishes, Matthias

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smaller cell volume for accommodating protein complex & no MR solution even very similar template
by 陈成 11 Jul '25

11 Jul '25

Dear PHENIXBB people, I have been working on several data sets collected from crystals grown in co-crystallization trials containing a small molecule and Calprotectin, a heterologous protein dimer comprised of two polypeptides with around 90 and 120 amino acids respectively. The crystallographic structure of Calprotectin complexed with a 18-aa peptide have been deposited in RCSB database under PDB entry 7QUV, with cell parameters a = b = 50.8, c = 148.8 in the P 32 2 1 space group. On the contrast, the bunches of data sets I collected give cell parameters a = b = 38.3, c = 196.3 in the P 6 2 2 space group when an oscilliation angle of 0.5 degree was used or cell parameters a = b = 38.2, c = 149.0 in the P 6 2 2 space group when an oscilliation angle of 0.2 degree was used. In either cases, Matthews_coef analysis would suggest that the crystal cell cannot accommodate the whole Calprotectin complex. I had used each single protein of Calprotectin as the search template for MR, but failed as well. Though Phenix.xtriage suggest nothing wrong with the data sets, however, considering that the two polypeptide conprising Calprotectin is structurally similar, I had also tried indexing the data sets under space group spanning P2, P3 apart from P622 and then run MR by a thorough combination of each data sets and different template choices, which, in opposition to what was expected, still gave no reliable MR solution. It's noteworthy that the diffraction pattern of my crytals seemingly showed that multi-crystal problem or other intrinsic growth defects might be underconsidered. In fact, I've been encountering the above crystallographic situation for 3 times recently, which all bear the following characteristics: (1) cell volume is far smaller than expected for containing targeted macromolecules (protein/DNA) that is used for crystallization. (2) no MR solution is achieved though MR template is extremely and sometimes 100% similar. (3) growth defects such as multi-crystal or fibrous diffraction problems possibly exist. Hopefully someone may have dealt with such issues before. Any suggestions is welcomed! Sincerely Chen PS: This message is also posted on CCP4BB. Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai District, Tianjin 300072, China

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Re: phenixbb Digest, Vol 234, Issue 7 (out of office)
by Elisabeth Laurent 01 Jul '25

01 Jul '25

Thank you for your e-mail. I am out of office until July 8th, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 1.7.25 21:16 >>> 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. Re: phenix install/splash screen issue (Hekstra, Doeke Romke) 2. Data uncertainty: Minimising it and characterising the uncertainty that remains (John R Helliwell) 3. Postdoc Position - Berkeley, California (Paul Adams) ---------------------------------------------------------------------- Message: 1 Date: Sun, 15 Jun 2025 16:51:46 +0000 From: "Hekstra, Doeke Romke" <doeke_hekstra(a)harvard.edu> Subject: [phenixbb] Re: phenix install/splash screen issue To: Billy Poon <BKPoon(a)lbl.gov> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <BL0PR07MB38897932A0F5134154C3D9199771A(a)BL0PR07MB3889.nam prd07.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Awesome. Will try later this week! -----Original Message----- From: Billy Poon <BKPoon(a)lbl.gov> Sent: Sunday, June 15, 2025 12:36 PM Cc: phenixbb(a)phenix-online.org Subject: [phenixbb] Re: phenix install/splash screen issue Hi Doeke, I got the GUI to work over VNC using ThinLinc at NERSC. The check used to work in Python 2 because comparing against None was allowed. I updated the code to skip the check if any value is None since it's not so crucial. I'll make another build available tomorrow. Let us know if you find any other issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sat, Jun 14, 2025 at 2:51 PM Hekstra, Doeke Romke < doeke_hekstra(a)harvard.edu> wrote: > Hi Billy, > > Correct, I’m using a remote desktop (open on demand, via vnc). > > Doeke > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Billy Poon <BKPoon(a)lbl.gov> > *Sent:* Saturday, June 14, 2025 12:19:00 AM > *To:* Hekstra, Doeke Romke <doeke_hekstra(a)harvard.edu> > *Cc:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] phenix install/splash screen issue > > Hi Doeke, > > Are you running over X or via a virtual desktop? I just tested over X > and the GUI shows up. I'm going to try a remote desktop next. > > The issue is that the GUI is unable to calculate some limit for > placing windows. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Fax: (510) 486-5909 > Web: https://phenix-online.org > <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline. > org&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMK > OIsdAAHocfxcg&m=E0acsYpZgOQ4jSQxX3QvM2W7a5egZssjBf25gnnV1q4CSsCigsm5eu > QXFzvdyEen&s=sNVrQKJJi4zo2EFXfPjtPYUxQ_hTsSQ0TT8vAPzd5Lg&e=> > > > On Sat, Jun 14, 2025 at 5:12 AM Hekstra, Doeke Romke < > doeke_hekstra(a)harvard.edu> wrote: > > Hi, > After an ostensibly error-free installation of phenix-2.0-5716 on > linux within an HPC environment, when starting the Phenix GUI, I get > the following error: > > [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: > Traceback (most recent call last): > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py"> Error.show_exception_dialog(type, value, traceback) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Err > or.py", > line 76, in show_exception_dialog > if (app.bug_timer.IsRunning() is False): > AttributeError: 'PhenixApp' object has no attribute 'bug_timer' > > Original exception was: > Traceback (most recent call last): > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 136, in OnInit > self.start_gui() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 151, in start_gui > self.get_screen_params() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 263, in get_screen_params > self.set_window_height(self.prefs.get_root().gui.max_dialog_height) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 266, in set_window_height > if (max_height < self.screen_height) : > TypeError: '<' not supported between instances of 'NoneType' and 'int' > OnInit returned false, exiting... > > ==== > The same error occurred with phenix-2.0-5716 (both using the > Linux-x86_64 installer). > > Could you please advise? > > Thanks, > Doeke > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe > send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > > _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 2 Date: Mon, 30 Jun 2025 12:34:53 +0100 From: John R Helliwell <jrhelliwell(a)gmail.com> Subject: [phenixbb] Data uncertainty: Minimising it and characterising the uncertainty that remains To: CCP4BB(a)jiscmail.ac.uk, PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <A26415F8-B11F-463A-B03F-F198BCAAA1AA(a)gmail.com> Content-Type: text/plain; charset=utf-8 Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc ------------------------------ Message: 3 Date: Tue, 1 Jul 2025 12:15:56 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Postdoc Position - Berkeley, California To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <19D7DA5E-15B5-4705-A591-4F28C2F4AC9B(a)lbl.gov> Content-Type: text/plain; charset=us-ascii Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- 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 PresidenPrincipal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.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 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 ] -- ------------------------------ 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 234, Issue 7 ****************************************

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Postdoc Position - Berkeley, California
by Paul Adams 01 Jul '25

01 Jul '25

Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- 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) 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 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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Data uncertainty: Minimising it and characterising the uncertainty that remains
by John R Helliwell 30 Jun '25

30 Jun '25

Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc

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phenix install/splash screen issue
by Hekstra, Doeke Romke 15 Jun '25

15 Jun '25

Hi, After an ostensibly error-free installation of phenix-2.0-5716 on linux within an HPC environment, when starting the Phenix GUI, I get the following error: [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 972, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 136, in OnInit self.start_gui() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 151, in start_gui self.get_screen_params() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 263, in get_screen_params self.set_window_height(self.prefs.get_root().gui.max_dialog_height) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 266, in set_window_height if (max_height < self.screen_height) : TypeError: '<' not supported between instances of 'NoneType' and 'int' OnInit returned false, exiting... ==== The same error occurred with phenix-2.0-5716 (both using the Linux-x86_64 installer). Could you please advise? Thanks, Doeke

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phenix.map_sharpening - sequence file required?
by Oliver Clarke 04 Jun '25

04 Jun '25

Hi, The new-ish map_sharpening utility seems to absolutely require a sequence file (at least on the CLI), whereas using auto_sharpen one could directly provide solvent content or estimated molecular mass. This option - molecular_mass - is still present in map_sharpening, but the program still terminates with an error - "Sorry: Need a sequence file". Is this intended? I run using the following command: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 molecular_mass=50000 Cheers Oli

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Reminder: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 02 Jun '25

02 Jun '25

Dear Colleagues, A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th 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 <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> October 12 - 28, 2025 Applications Due: July 15 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 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) For further information and to apply please visit the Macromolecular Crystallography course website. <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> 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%3D&…> | Update Profile <https://visitor.constantcontact.com/do?p=oo&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | 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) 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 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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Windows 10 Retirement Date
by Billy Poon 26 May '25

26 May '25

Hi everyone, Microsoft will be dropping support for Windows 10 later this year on October 14, 2025. https://learn.microsoft.com/en-us/lifecycle/products/windows-10-home-and-pro Phenix intends to drop Windows 10 support after that date. Are there users where Windows 10 support is required after that date? Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: map-to-model FSC on low resolution map
by Pavel Afonine 26 May '25

26 May '25

Hi Jesse, there was a bug a while ago that we fixed. Are you using the latest Phenix? If not, please try it and if that does not fix the problem we'll take a closer look. All the best! Pavel On 5/26/25 08:07, bluufive2--- via phenixbb wrote: > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

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