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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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