- phenixbb - phenix-online.org

Cryo_fit installation
by omar.debei＠unipr.it 28 Feb '25

28 Feb '25

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

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Register by Feb. 28th for the West Coast Structural Biology Workshop
by Michael Thompson 21 Feb '25

21 Feb '25

The registration and abstract submission deadlines for the 26th West Coast Structural Biology Workshop are just one week away... Register today, and be a part of this iconic meeting with over 50 years of tradition!! See below for a message about the conference: Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025. The meeting is scheduled for March 23-26, 2025 at its traditional location, the 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. * 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). 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 February 28, 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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Postdoc and PhD positions in quantum/protein/electron crystallography. Application deadline March 2nd
by Paulina Dominiak 03 Feb '25

03 Feb '25

Dear Colleagues, We currently have several positions available in my group at the University of Warsaw - both postdoc and PhD. The research project combines quantum crystallography with protein crystallography, focusing on 3DED/microED techniques. We're interested in hearing from researchers with different backgrounds: * Software developers who want to learn crystallography * Protein crystallographers looking to expand their skills * Small-molecule crystallographers experienced with X-ray charge density studies * Researchers familiar with electron crystallography Detailed information about the positions, project description, and application links can be found at: http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/ <http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/> Application deadline: March 2nd, 2025 Please share this opportunity with qualified candidates who might be interested. For additional information, feel free to contact me directly. Best regards, Paulina -- Prof. dr hab. Paulina M. Dominiak Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail:[email protected] Phone: (48) 22 55 26 714 WWW:http://4xeden.uw.edu.pl

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DEADLINE EXTENDED: 26th West Coast Structural Biology Workshop
by Michael Thompson 03 Feb '25

03 Feb '25

Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025 and Feb. 21, 2025 respectively. The meeting is scheduled for March 23-26, 2025 at its traditional location, the 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. * 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). 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 February 21, 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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Re: Uknown non bonded
by Yann Lefrançois.C 30 Jan '25

30 Jan '25

Hi thank you for your reply, I'm not working with ligand, but a complexe. I do not have hydrogen in my model, so it seems I have a bigger problem. [image: image.png] I tried to use PDB_REDO, however i'm using mrc format for my ED map Le jeu. 30 janv. 2025 à 16:39, Georg Mlynek <georg.mlynek(a)univie.ac.at> a écrit : > Hi Yann, can you post a screenshot of the error message? It should be > stated there which are causing problems. > > Very often the problems are hydrogens. So just delete those. One easy > way is to do is to open in coot and when saving there is a tick box > without hydrogens. There are also tools in phenix doing this. > > Also you can submit the pdb to PDB_REDO to check if there are more sever > problems. If PDB_REDO runs then there are no big errors. Then just use > the output for phenix refine. > > And as Xavier wrote ligands also can cause problems. But also there most > times the hydrogens. > > Br, Georg. > > > Am 2025-01-30 um 4:26 PM schrieb yannlefrancoiscopy(a)gmail.com: > > Hello, > > I'm a newbie phenix user, and i was trying to refine a model. > > > > and when i tried to refine it, I got an error message saying that some > atoms had unknown nonbonded interaction. > > > > However, there are no indication to which one are problematic, Any tips > on how to find the problematic one and how to correct them ? > > > > best wishes, > > Yann > > _______________________________________________ > > 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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Uknown non bonded
by yannlefrancoiscopy＠gmail.com 30 Jan '25

30 Jan '25

Hello, I'm a newbie phenix user, and i was trying to refine a model. and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction. However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them ? best wishes, Yann

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open position for a 2(+2) year postdoc working on plant sugar and hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 29 Jan '25

29 Jan '25

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of sugar and hormone transport, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 28. Feb. 2025 using the online application system (link above).

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Reminder: Phenix Postdoc Position - Berkeley, California
by Paul Adams 27 Jan '25

27 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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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About d99
by Roberto Battistutta 24 Jan '25

24 Jan '25

Dear Phenix people, In "New tools for the analysis and validation of cryo-EM maps and atomic models” (ActaD 2018), it is reported that "map sharpening can affect d99 (Fig. 9g) but it is rather insensitive to masking (Fig. 9h).” I have a case where d99 increases a lot with masking, as shown in the screenshot below (from Mtriage). On the other hand, FSC decreases. What does this mean? Can it be attributed to the fact that there is a strong scatterer in the molecule (a heavy atom) that strongly influences the intensity of the map? Are there other possible explanations (preferential orientation for example)? What is the best way to handle such maps? Thank you for the attention. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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André Mitschler, former crystallography engineer in the BSI department, Strasbourg
by Alexandre OURJOUMTSEV 24 Jan '25

24 Jan '25

Sorry, my previous e-mail left with a wrong subject… Sacha = = = = Dear all, for those (I expect, many of you) who knew André Mitschler, I resubmit the message below. Sad news. It was a great and non-trivial person. With best wishes, Sacha Urzhumtsev = = = = From: Valerie LAMOUR <lamourv(a)igbmc.fr<mailto:[email protected]>> Sent: Friday, January 24, 2025 4:23 PM Subject: André Mitschler, former crystallography engineer in the BSI department André Mitschler est décédé le 5 Décembre, à l’âge de 83 ans. André était un cristallographe expérimental hors pair. Il a débuté en recherche dans le laboratoire du Prof Weiss où il a eu la charge du premier diffractomètre à RX de l’époque. En 1967, a entamé une fructueuse collaboration avec Dino Moras qui a pu bénéficier de son expertise et son adresse expérimentale pour sa thèse de 3e cycle. Leurs liens ne se sont jamais rompus. En 1981 Il a rejoint le laboratoire de cristallographie de Dino, nouvellement créé à l’IBMC. Il y a effectué le reste d’une fructueuse carrière d’ingénieur CNRS qui, en 1994, s’est poursuivie à l’IGBMC, un nouvel institut créé à Illkirch avec un important soutien de l’industrie pharmaceutique. En 1996, il a rejoint le groupe d’Alberto Podjarny, pour travailler dans la détermination de la structure de l’Aldose Reductase humaine. Les cristaux diffractaient à une résolution extrêmement haute (0.6 Angstroms). La mesure des données a demandé des nouveaux développements et l’utilisation des meilleures lignes synchrotron du monde. André était à la hauteur du défi, avec la capacité de passer de longues heures à monter et tester expérimentalement des cristaux. Il pouvait travailler 72 heures d’affilée dans le synchrotron d'Argonne National Lab. Le travail a culminé en 2008, avec la publication d’un mécanisme enzymatique inattendu. En 1999, il a obtenu la médaille de Cristal du CNRS, en reconnaissance de ses travaux en cristallographie expérimentale. André était aussi un passionné de l’histoire militaire, et a fait une carrière dans l’armée jusqu’à rang de colonel dans la cavalerie. Sa passion par la recherche, sa force de travail et son dévouement pour l’excellence expérimentale sont un exemple à suivre par tous les jeunes chercheurs. //// André Mitschler passed away on December 5th at the age of 83. André was an outstanding experimental crystallographer. He began his research career in Professor Weiss's laboratory, where he was responsible for the first X-ray diffractometer at the time. In 1967, he started a fruitful collaboration with Dino Moras, whose doctoral work benefited greatly from André's expertise and experimental skill. Their professional ties endured throughout their lives. In 1981, André joined Dino’s newly established crystallography laboratory at IBMC, where he spent the remainder of a productive career as a CNRS engineer. In 1994, he continued his work at IGBMC, a new institute in Illkirch supported by the pharmaceutical industry. In 1996, André joined Alberto Podjarny’s group to work on determining the structure of human aldose reductase. The crystals diffracted at an exceptionally high resolution (0.6 Å), which required innovative developments and access to the world's most advanced synchrotron beamlines. André rose to the challenge, demonstrating his ability to spend long hours preparing and experimentally testing crystals. He worked tirelessly, including 72-hour shifts at the Argonne National Laboratory synchrotron. This effort culminated in 2008 with the publication of an unexpected enzymatic mechanism. In 1999, André was awarded the CNRS Crystal Medal in recognition of his contributions to experimental crystallography. André was also a military history enthusiast and pursued a parallel career in the army, rising to the rank of colonel in the cavalry. His passion for research, tireless work ethic, and dedication to experimental excellence remain an inspiration for young researchers.

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 24 Jan '25

24 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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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Error in Windows installation: Phenix 1.21.2-54
by Jobichen Chacko 18 Jan '25

18 Jan '25

ImportError : __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 22, in import_ext try: mod = __import__(name) ImportError: DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\MainWindow.py", line 745, in <lambda> menu.add_command("Run now", lambda evt: self.run()) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 426, in run self.start_process(config_file, output_dir, process_type) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Templates.py", line 701, in start_process run_notebook = self.create_run_notebook() File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 532, in create_run_notebook from wxGUI2.Programs.Refine import Output File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Output.py", line 5, in <module> from wxGUI2 import GLViewer, AdvancedWidgets, Buttons File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\GLViewer.py", line 10, in <module> from crys3d.wx_combined_viewer import viewer_phil File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_combined_viewer.py", line 4, in <module> from crys3d.wx_selection_editor import selection_editor_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_selection_editor.py", line 6, in <module> from crys3d.wx_model_viewer import model_scene, model_viewer_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_model_viewer.py", line 10, in <module> from gltbx.wx_viewer import wxGLWindow File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\wx_viewer.py", line 8, in <module> from gltbx.glu import * File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\glu.py", line 3, in <module> ext = bp.import_ext("gltbx_glu_ext") File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 31, in import_ext raise ImportError( Dear All, I am getting this error when trying to run Phenix-refine. Any idea how to fix this? Thank you. Jobi ImportError: __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename

2 3

Error opening REEL and ligand refinement in Coot
by Marian Oliva 17 Jan '25

17 Jan '25

Dear all, I posted this problem a couple of days ago through phenix help mail address but I got no answer (not sure if it was delivered properly). Maybe here I am luckier. I have recently upgrade my machine to Ubuntu MATE 1.26 and re-install all crystallography software I often use, including Phenix version dev-5493. I am working in a structure of a protein bound to a new ligand. I built the ligand with chemDraw, get the SMILE, get a universal SMILE string in cactus.nci.nih.gov <http://cactus.nci.nih.gov/>, and used eLbow for ligand restraints generation and optimization (using default parameters). First problem. When I try to open the ligand in REEL. Phenix crash with the following message in the terminal libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so <http://swrast_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast The program 'main.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue'. (Details: serial 39668 error_code 2 request_code 152 minor_code 24) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) Second, when I open the structure in Coot (0.9.8.95) from Phenix and try to perform real space refine zone to the ligand, the attached window pops-up. Is this because I did something wrong during the installation? Is there a bug I am not aware of? Any help will be really appreciate. Many thanks in advance, Marian

1 0

mmtbx.ringer with noise maps
by Schulz, Dr. Eike 15 Jan '25

15 Jan '25

Hi everyone, I am using mmtbx.ringer via phenix-1.21rc1-5127 to explore ED changes from END/RAPID maps. While it’s possible to provide volume scaled maps, it does seem possible to provide noise maps from END/RAPID is that correct or am I missing sth.? Related: setting gui=true enables to graphically browse through the results, it does not seem to be possible to automatically save all these plots. Is it possible to activate this? Best regards, Eike

1 0

phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by fnsoxt＠qq.com 09 Jan '25

09 Jan '25

How can i deal with it? This is the log file Starting phenix.predict_and_build on Wed Jan 1 20:55:50 2025 by xukui =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta resolution=4.1 nproc=20 predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb process_predicted_model.chunk_size=10000 predict_and_build.chunk_size=10000 process_predicted_model.break_into_chunks_if_length_is=10000 predict_and_build.break_into_chunks_if_length_is=10000 Warning: Ambiguous parameter definition: resolution = 4.1 Best matches: crystal_info.resolution prediction.resolution Assuming crystal_info.resolution was intended. Warning: Ambiguous parameter definition: nproc = 20 Best matches: prediction.nproc control.nproc Assuming control.nproc was intended. Processing files from PHIL: ------------------------------------------------------------------------------- Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" model { file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } default_model = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } predict_and_build { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } input_files { seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta map_model { full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc } predicted_model = /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb } crystal_info { resolution = 4.1 } process_predicted_model { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } control { nproc = 20 } Starting job =============================================================================== ************************************************************ PHENIX predict_and_build Wed Jan 1 20:55:59 2025 ************************************************************ Working directory: /data2/xukui/data/jobs_pab/6b3o PHENIX VERSION: 1.21.1-5286 Base directory is /data2/xukui/data/jobs_pab/6b3o Creating jobname of 'PredictAndBuild_0' Working directory /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created in base directory Output prefix for files will be: /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt Running in Standard mode... Turning off all building steps except refinement Running with a cryo-EM map Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 Added predicted model /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with plddt=80.96 Mean value in B-factor field for /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from plddt to plddt): 80.96 Set random_seed_iterations to 5 No templates read from templates_as_string... Total of 0 templates to be used Setting density_modify_with_model = False (default for cryo-EM) Set rmsd_for_similar_placement to 4.10 A Working directory will be based on jobname: PredictAndBuild_0 Created new temp dir: PredictAndBuild_0 ... temp-dir will be deleted at end ================================================================================ Running predict_and_build ================================================================================ Starting data: Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift (0, 0, 0) Working coordinate shift (-0.0, -0.0, -0.0) NCS object with 0 groups: List of sequences: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK List of models: af2_group_0.pdb Chain A extracted List of chain IDs and sequences to use A (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK B (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK C (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running cycle 1 of predict_and_build ================================================================================ Not using any supplied msas No supplied templates will be used in prediction this cycle ================================================================================ Predicting models for 0 chains with alphafold Updating chain names in model list... Chain A: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Total of 1 working models Total MSAs obtained: 0 Updating chain IDs Previous ID: 'A' New ID: 'A' MODEL: af2_group_0.pdb Getting processed (trimmed, B-values updated) models B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model from af2_group_0.pdb with 492 residues (of 605) =============================================================================== Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== =============================================================================== Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== Checking whether scaffold model is complete... ================================================================================ Getting new scaffold model in /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb ================================================================================ ================================================================================ Docking 1 models (to represent 3 sequences) in map to create a scaffold ================================================================================ Model to dock: af2_group_0.pdb: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Calculating how many copies of each sequence Model: A MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Model copies: 1 Sequence copies: 3 Remainder copies: {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': 0} remainder: 0 Copies to use: 3 Setting up model for dock_and_rebuild Added model af2_group_0.pdb (A) for dock_and_rebuild Running dock_and_rebuild to dock models Total of 1 predicted models MODEL: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running dock_and_rebuild on total of 3 chains Chain 1 (chain A from af2_group_0.pdb) Chain 2 (chain A from af2_group_0.pdb) Chain 3 (chain A from af2_group_0.pdb) ================================================================================ ================================================================================ Running on chain 1 (chain A from af2_group_0.pdb) ================================================================================ Working directory for this chain: PredictAndBuild_0/local_dock_and_rebuild_1_0 No docked model for chain A ... Running search... Running standard docking... =============================================================================== Processing input model =============================================================================== B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model with 492 residues (of 605) Wrote processed model to /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb =============================================================================== Extracting unique part of map =============================================================================== Setting map-model-manager and model shift to zero during run Split model into chains: A1 Chain number: 1 id: A1 Residues: 492 ============================================================================== Searching with each chain as a seed ============================================================================== ============================================================================== Running dock-in map on domain A1 with 492 residues ============================================================================== Running dock-in-map at overall resolution of 4.1 A Density radius set to: 24.6 A Placing model in map Map has been not been offset New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, 90.00) Target boxes set to 20 Choosing local part of search model to use in search... Shifting search model coordinates (0.3, 1.9, -1.9) to origin and creating search map coefficients Docking with MR... Using masked map data MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) Estimated solvent fraction: 0.95 Total atoms in all copies: 3781 (volume = 66567.6 A**3) Solvent fraction (as used) is about 0.94 Total good sites: 11268 Max clusters: 1 Wrote mtz data to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz Wrote model A1_full_shifted_sm_1.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb Wrote model A_from_cluster_0.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb

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Re: phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by Tom Terwilliger 09 Jan '25

09 Jan '25

On Thu, Jan 9, 2025 at 11:13 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote: > Hi Tom, > > I fished out the following from my Spam folder, but it is on PhenixBB. Can > you please take a look? > > Best regards, > Oleg Sobolev. > > ---------- Forwarded message --------- > From: <fnsoxt(a)qq.com> > Date: Sun, Jan 5, 2025 at 8:03 PM > Subject: [phenixbb] phenix.predict_and_build, proccess normal and no > error, but not generate the PredictAndBuild_0_overall_best.pdb > To: <phenixbb(a)phenix-online.org> > > > How can i deal with it? This is the log file > > Starting phenix.predict_and_build > on Wed Jan 1 20:55:50 2025 by xukui > > =============================================================================== > > Processing files: > > ------------------------------------------------------------------------------- > > No files found > > Processing PHIL parameters: > > ------------------------------------------------------------------------------- > > Adding command-line PHIL: > ------------------------- > full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > resolution=4.1 > nproc=20 > > predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > process_predicted_model.chunk_size=10000 > predict_and_build.chunk_size=10000 > process_predicted_model.break_into_chunks_if_length_is=10000 > predict_and_build.break_into_chunks_if_length_is=10000 > > Warning: Ambiguous parameter definition: resolution = 4.1 > Best matches: > crystal_info.resolution > prediction.resolution > Assuming crystal_info.resolution was intended. > Warning: Ambiguous parameter definition: nproc = 20 > Best matches: > prediction.nproc > control.nproc > Assuming control.nproc was intended. > Processing files from PHIL: > > ------------------------------------------------------------------------------- > > Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > > Final processed PHIL parameters: > > ------------------------------------------------------------------------------- > data_manager { > sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > model { > file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > default_model = > "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > predict_and_build { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > input_files { > seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > map_model { > full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > } > predicted_model = > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > } > crystal_info { > resolution = 4.1 > } > process_predicted_model { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > control { > nproc = 20 > } > > > Starting job > > =============================================================================== > > ************************************************************ > PHENIX predict_and_build Wed Jan 1 20:55:59 2025 > ************************************************************ > > Working directory: /data2/xukui/data/jobs_pab/6b3o > > PHENIX VERSION: 1.21.1-5286 > > Base directory is /data2/xukui/data/jobs_pab/6b3o > Creating jobname of 'PredictAndBuild_0' > Working directory > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created > in base directory > Output prefix for files will be: > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt > Running in Standard mode... > Turning off all building steps except refinement > > Running with a cryo-EM map > Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 > Added predicted model > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with > plddt=80.96 > Mean value in B-factor field for > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from > plddt to plddt): 80.96 > Set random_seed_iterations to 5 > No templates read from templates_as_string... > Total of 0 templates to be used > Setting density_modify_with_model = False (default for cryo-EM) > > Set rmsd_for_similar_placement to 4.10 A > Working directory will be based on jobname: PredictAndBuild_0 > Created new temp dir: PredictAndBuild_0 ... > temp-dir will be deleted at end > > > ================================================================================ > Running predict_and_build > > ================================================================================ > > Starting data: > Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) > Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), > Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift > (0, 0, 0) > Working coordinate shift (-0.0, -0.0, -0.0) > NCS object with 0 groups: > > List of sequences: > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > List of models: > af2_group_0.pdb Chain A extracted > > List of chain IDs and sequences to use > A (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > B (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > C (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running cycle 1 of predict_and_build > > ================================================================================ > Not using any supplied msas > No supplied templates will be used in prediction this cycle > > > ================================================================================ > Predicting models for 0 chains with alphafold > > Updating chain names in model list... > Chain A: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Total of 1 working models > Total MSAs obtained: 0 > > Updating chain IDs > Previous ID: 'A' New ID: 'A' > MODEL: af2_group_0.pdb > > Getting processed (trimmed, B-values updated) models > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model from af2_group_0.pdb with 492 residues (of 605) > =============================================================================== > > Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > =============================================================================== > > Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > > Checking whether scaffold model is complete... > > > > ================================================================================ > Getting new scaffold model in > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb > > ================================================================================ > > > ================================================================================ > Docking 1 models (to represent 3 sequences) in map to create a scaffold > > > ================================================================================ > Model to dock: af2_group_0.pdb: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Calculating how many copies of each sequence > Model: A > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Model copies: 1 Sequence copies: 3 > Remainder copies: > {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': > 0} remainder: 0 > Copies to use: 3 > Setting up model for dock_and_rebuild > Added model af2_group_0.pdb (A) for dock_and_rebuild > > Running dock_and_rebuild to dock models > > Total of 1 predicted models > MODEL: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running dock_and_rebuild on total of 3 chains > Chain 1 (chain A from af2_group_0.pdb) > Chain 2 (chain A from af2_group_0.pdb) > Chain 3 (chain A from af2_group_0.pdb) > > ================================================================================ > > > ================================================================================ > Running on chain 1 (chain A from af2_group_0.pdb) > > ================================================================================ > Working directory for this chain: > PredictAndBuild_0/local_dock_and_rebuild_1_0 > No docked model for chain A ... > Running search... > > Running standard docking... > > =============================================================================== > > Processing input model > =============================================================================== > > > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model with 492 residues (of 605) > Wrote processed model to > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb > > =============================================================================== > > Extracting unique part of map > =============================================================================== > > > > Setting map-model-manager and model shift to zero during run > Split model into chains: A1 > Chain number: 1 id: A1 Residues: 492 > > ============================================================================== > > Searching with each chain as a seed > ============================================================================== > > > > ============================================================================== > > Running dock-in map on domain A1 with 492 residues > ============================================================================== > > > > Running dock-in-map at overall resolution of 4.1 A > Density radius set to: 24.6 A > Placing model in map > > Map has been not been offset > New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, > 90.00) > Target boxes set to 20 > > Choosing local part of search model to use in search... > > Shifting search model coordinates (0.3, 1.9, -1.9) to origin > and creating search map coefficients > > Docking with MR... > Using masked map data > MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) > Estimated solvent fraction: 0.95 > Total atoms in all copies: 3781 (volume = 66567.6 A**3) > Solvent fraction (as used) is about 0.94 > Total good sites: 11268 > Max clusters: 1 > Wrote mtz data to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz > Wrote model A1_full_shifted_sm_1.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb > Wrote model A_from_cluster_0.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb > _______________________________________________ > 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 > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

1 0

Error phenix refine with ligands
by miriam.cavinato＠unimi.it 07 Jan '25

07 Jan '25

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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26th West Coast Structural Biology Workshop - March 23-26, 2025 @ Asilomar Conference Center
by Michael Thompson 06 Jan '25

06 Jan '25

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…>

1 0

Handling of modified nucleotides in ribosome structures
by christian.steinmetzger＠imbim.uu.se 19 Dec '24

19 Dec '24

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

4 9

cryo em map
by iram aziz 18 Dec '24

18 Dec '24

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

5 4

PostDoc and Associate Researcher positions in structural biology field at ISMMS in NYC
by Wang, Wei 13 Dec '24

13 Dec '24

Dear all, I'd like to draw your attention to the availability of postdoctoral and associate researcher positions in my newly started lab at Icahn School of Medicine at Mount Sinai in New York City. Our lab focuses on elucidating protein dynamics and functions under disease-related conditions, with a strong collaborative tie to the Mount Sinai Center for Transformative Disease Modeling. I hereby sincerely invite colleagues to join my lab for the mutual research interest. For more details on the available positions and the application process, please visit the following links: Postdoctoral candidate please visit: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postd… Associate Researcher candidate please visit: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-assoc… Please don't hesitate to reach out if you have any questions. I would be glad to talk with you. Wei Wang, PhD Assistant Professor Department of Genetics and Genomic Sciences Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai e: wei.wang(a)mssm.edu<mailto:[email protected]>

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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 05 Dec '24

05 Dec '24

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)

1 4

Phenix error in real space refinement with ligand
by Yung-Chieh Chen 03 Dec '24

03 Dec '24

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

2 1

Polder map
by jirivitali＠gmail.com 27 Nov '24

27 Nov '24

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

2 1

open position for a 2(+2) year postdoc working on plant hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 25 Nov '24

25 Nov '24

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of auxin transport, Aarhus University, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on auxin hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 20. Dec. 2024. See details here: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral…

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PostDoc position in time resolved serial crystallography at ESRF ID29 beamline
by Daniele de Sanctis 15 Nov '24

15 Nov '24

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.

1 0

Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 31 Oct '24

31 Oct '24

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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Tool to calculate Q-scores?
by Guillaume Gaullier 29 Oct '24

29 Oct '24

Hello phenixbb, It would be convenient to have a tool to calculate Q-scores [1], with suggested command-line name phenix.qscore or phenix.model_map_qscore. It would work just like phenix.model_map_cc but report Q-scores instead (average per chain by default, but if requested also per-residue backbone / side chain / whole residue averages, or per ligand). And phenix.validation_cryoem could report these scores as well, in addition to the CCs that it already reports. There is already a tool to do this in ChimeraX [2], which is very helpful for interactive work. But for automated calculation of these scores from many models and maps, it would be more convenient to have a phenix tool for it. If it already exists, sorry I overlooked it (but I looked up both the latest documentation and phenix command completion and couldn't find anything like it), and I'll be happy if somebody can point me to it! Cheers, Guillaume [1]: https://doi.org/10.1038/s41592-020-0731-1 [2]: https://github.com/tristanic/chimerax-qscore När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

1 0

MASSIF-1 10 year celebration symposium
by Matthew BOWLER 25 Oct '24

25 Oct '24

Dear CCP4 community, I would like to draw your attention to a one day symposium we are holding here in Grenoble to celebrate 10 years of fully automatic data collection at the ESRF/EMBL beamline MASSIF-1 - from starting with basic characterisation and data collection we now measure crystal volumes, dynamically adapt beam diameters, automatically collect and merge kappa sweeps, helical and multi-crystal data sets and even automatically mount crystals from trays using the EMBL CrystalDirect robot. With a great line-up of speakers we will highlight some of the research enabled by MASSIF-1, how it has inspired other beamlines around the world, as well as some history of the project. You can find more details in the attached flyer and register in the link below. We look forward to seeing you in Grenoble! Matthew Bowler and Didier Nurizzo. https://www.esrf.fr/home/events/conferences/2024/massif-1-symposium.html -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/mbowler/ ===================================================

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Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 25 Oct '24

25 Oct '24

Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay.  This is because we have had a number of students obtaining bursaries and then cancelling last minute.  Places can be transferred to other people at no charge.  Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp4sw(a)stfc.ac.uk<mailto:[email protected]> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:[email protected]] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30**********

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working with composite models
by Dmitry Semchonok 24 Oct '24

24 Oct '24

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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About cryo-EM map sharpening in Phenix
by Shanti Pal Gangwar 16 Oct '24

16 Oct '24

Hello everyone, I'm working on anisotropic map sharpening in Phenix version 1.21-5207-00 with a cryo-EM map of a multiprotein complex. Should I provide the sequence files for each component individually, or would it be better to compile all the sequences into a single file? In addition, shall I provide the full sequence even if a segment of the protein is not resolved in the map? I would appreciate any advice! Shanti Pal

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AQuaRef - issues with torch-cluster installation
by Martin Malý 16 Oct '24

16 Oct '24

Dear colleagues, I'm trying to install AQuaRef. However, I'm struggling with running `bash config/update_phenix.sh aimnet2` which is part of `bash build_into_phenix.sh aimnet2`. This script wants to install the python package torch-cluster. However, I'm getting the error: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] I'm getting the same error when I tried to install only this package using the command `qrefine.python -m pip install torch-cluster`. I have a laptop with Ubuntu 22.04. I have all the usual development packages installed (build-essential, linux-headers, gcc, g++, ...). According Python, I have libpython3-dev, libpython3.10-dev, python3-dev, python3.10-dev. I can see that qrefine.python has a version of 3.9, so I also installed libpython3.9-dev, python3.9-dev and python3.9-distutils from ppa:deadsnakes/ppa but it did not help. I am also attaching a full log from the torch-cluster installation. It seems that the package torch has been installed successfully in prior. Do you have please an idea what is wrong and how to fix it? Thank you. Martin

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help for the 4.3 A dataset
by princeadam＠163.com 15 Oct '24

15 Oct '24

Dear colleagues, I am currently engaged in an endeavor to unravel the crystal structure through molecular replacement techniques. Regrettably, the resolution attained stands at a rather low mark, approximately 4.3 Angstroms, which poses significant challenges. Despite exhaustive efforts directed towards optimizing the crystal conditions, there has been no discernible improvement in the resolution. The structure in question is confined to a specific domain, and we have at our disposal two distinct conformational models sourced from the PDB database: one derived from X-ray data and the other from Cryo-EM. Our prime objective is to meticulously discern which of these two conformations aligns most accurately with our experimental context. To this end, we have employed both structures (X-ray and Cryo-EM) as templates for molecular replacement, yet the refinement process has hit a roadblock, hindering our progress. We are seeking a collaborator with experience in dealing with low-resolution data to assist in solving the structure. We are open to sharing first or corresponding authorships in the near future for this paper. Warm regards Hui

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NIH would like your input
by Paul Adams 14 Oct '24

14 Oct '24

Dear Colleagues, For those of you in the US, you might want to know that NIH issued a Request for Information about their National Resources and Biomedical Technology Optimization and Dissemination programs: https://www.research.net/r/NRRs_and_Biomedical_Technology_Optimization_and_… Unfortunately, it closes tomorrow, but it is a short form. They are interested in experiences with existing resources, but are most interested in hearing ideas for expanding the programs to new technologies. Currently funded resources can be found here: https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regi… Information about the Biomedical Technology Optimization and Dissemination program can be found here: https://www.nigms.nih.gov/grants/Pages/btod.aspx NIH would appreciate your thoughts about additional technologies that would benefit the community by support through these programs. 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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NIH would like your input
by Paul Adams 14 Oct '24

14 Oct '24

Dear Colleagues, For those of you in the US, you might want to know that NIH issued a Request for Information about their National Resources and Biomedical Technology Optimization and Dissemination programs: https://www.research.net/r/NRRs_and_Biomedical_Technology_Optimization_and_… Unfortunately, it closes tomorrow, but it is a short form. They are interested in experiences with existing resources, but are most interested in hearing ideas for expanding the programs to new technologies. Currently funded resources can be found here: https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regi… National Institute of General Medical Sciences nigms.nih.gov Information about the Biomedical Technology Optimization and Dissemination program can be found here: https://www.nigms.nih.gov/grants/Pages/btod.aspx NIH would appreciate your thoughts about additional technologies that would benefit the community by support through these programs. 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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Building Rosetta for Phenix
by Martin Malý 14 Oct '24

14 Oct '24

Dear colleagues, I am dealing with a low resolution data set (~4 A, protein crystal structure) so I would like to explore phenix.rosetta_refine. I followed the instructions at https://phenix-online.org/documentation/reference/rosetta_install.html . I applied the patch in ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings . After several minutes of compilation (command rosetta.build_phenix_interface), I got an error. I re-run the command to get a log file which I'm attaching. Please don't you have any idea what's wrong? I use Ubuntu 22.04. Thank you. Best regards, Martin

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Temperature shift alters unit cell of insulin: an issue
by Esra A 09 Oct '24

09 Oct '24

Dear Phenix community, I performed a temperature shift data collection for di-hexamer insulin. I collected single crystal data at 100K, 200K, and 300K, respectively After processing the data, I noticed that the unit cell of the 100K dataset is distinct from 200K and 300K. 100K dataset = 78.2182 78.2182 79.3565 90 90 120 (assume that this is di-hexamer) 200K dataset = 78.3157 78.3157 39.6367 90 90 120 (it is hexamer) 300K dataset = 80.7109 80.7109 39.6399 90 90 120 (it is hexamer) Even if I completed the structure determination of 200K and 300K successfully, I couldn't complete the molecular replacement of the 100K dataset due to the "*The composition entered will not fit in the unit cell volume*" error message. I tried every "copies" and "mass" parameter in *automr *script. However, i got the error message every run. I can share with you the mtz and reference pdb file, if needed. Could you help me, please? Where am I making a mistake? Thank you very much. Sincerely, Esra Ayan

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real space refine ADPs
by Leonid Sazanov 08 Oct '24

08 Oct '24

Hi, according to online description phenix.real_space_refine should refine only group ADPs per residue. However, in practice after the run with ADP included in strategy the recent versions refine individual B-factors per atom. They seem to look OK, but I wonder if this is a beta feature or fully implemented by now? Many thanks Leonid -- Prof. Leonid Sazanov FRS Institute of Science and Technology Austria (ISTA) Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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new BUILT of XDS
by kay.diederichs＠uni-konstanz.de 04 Oct '24

04 Oct '24

Dear XDS users in the Phenix community, as reported by users, and confirmed in a larger-scale comparison by GlobalPhasing, the BUILT=20240723 of XDS Version 20240630 leads to problems for some datasets when compared with (the expired) XDS Version 20230630. (it may be better than the 20230630 version for other datasets!). An improved BUILT=20241002 of the 20240630 version is available (all platforms) from https://xds.mr.mpg.de/html_doc/downloading.html for non-commercial (academic) users (commercial users have their own arrangements). In my/our testing, it is at least as good as version 20230630, and often better. Please install and use this instead of BUILT=20240723. If you still find deficiencies, please contact me or Wolfgang Kabsch - but be prepared to share the raw data (confidentially, of course). To enable comparisons, the old XDS version 20230630 was re-released for Linux by Wolfgang Kabsch with expiration date 2025-Mar-31; the link to its XDS_old.tar.gz is at https://xds.mr.mpg.de/ . Best wishes, Kay

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Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 03 Oct '24

03 Oct '24

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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ResolveCryoEM inputs
by Josh Cofsky 17 Sep '24

17 Sep '24

Hi, I'm attempting to run ResolveCryoEM, and I have a few questions about setting the job up correctly. My half-maps were reconstructed with C4 symmetry to ~2 Å (CryoSPARC), and my model was refined into the density with the "Ncs constraints" box checked (Phenix RSR). My sample is a protein-DNA complex (4 copies of a protein protomer, 4 copies of a ssDNA protomer). I'm running Phenix 1.21.1-5286-000 (the latest installation provided by SBGrid). In the first version of the run, I only supplied the two half-map files and a seq file. Question 1: My current seq.dat file looks like this (as mentioned previously in the forum, I was getting errors when I tried the version where my seq.dat file has only 1 protomer and I set the number of copies to 4 in the GUI field "Copies of sequence file in map"): >protein_protomer1 MGSRSG... >protein_protomer2 MGSRSG... >protein_protomer3 MGSRSG... >protein_protomer4 MGSRSG... >DNA_protomer1 AAAAAA >DNA_protomer2 AAAAAA >DNA_protomer3 AAAAAA >DNA_protomer4 AAAAAA Currently, Phenix is reading in the "AAAAAA" as a protein chain ("Chain types considered: PROTEIN"). How do I tell Phenix that those are deoxyadenosines, not alanines? Question 2: Is Phenix automatically detecting the C4 symmetry and density-modifying with that constraint? The resulting map looks symmetric in the noise, but I don't see anything in the log suggesting that it knows the symmetry. Here are some settings from the log that seem relevant (all left to default values): refine_symmetry_in_denmod = True use_symmetry_in_denmod = False symmetry_in_denmod_last_cycle_only = True fraction_ncs = None I attempted to supply a symmetry file (the output of a MapSymmetry job on the full map = "symmetry_from_map.ncs_spec"), but the file fails to load into the input ("Phenix error: Phenix did not recognize the file type for ****/symmetry_from_map.ncs_spec"). Question 3: A part of my protein is disordered and does not appear in the cryo-EM density (and was thus left unmodeled). Is it correct to leave that piece out of the seq.dat file? Question 4: If I include a model in the input, Phenix demands a symmetry file, but I couldn't get my symmetry file to load as explained above. What is the symmetry file supposed to look like? Thank you! -Josh

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Ordered solvent in phenix.refine
by Oliver H. Weiergräber 11 Sep '24

11 Sep '24

Hello, after switching from version 1.20 to 1.21, I noticed that the updated list of waters generated by the ordered_solvent option in phenix.refine is no longer numbered sequentially; it seems a final re-numbering step is now skipped. Is this intentional? Of course it can be advantageous to keep waters from changing their numbers, e.g. if they are part of occupancy groups. On a related note, is there a mechanism to protect certain "important" waters from being deleted while all the rest is updated as usual? One obvious option would be a dedicated chain ID, but afaik phenix.refine accepts a chain ID for output but not for input waters ... Best regards, Oliver ================================================== Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ==================================================

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Phenix version 1.21.2 released
by Paul Adams 05 Sep '24

05 Sep '24

The Phenix developers are pleased to announce that version 1.21.2 of Phenix is now available (build 1.21.2-5419). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this bug fix 1.21.2 version of Phenix include: - Fix issue where X-ray data parameters (e.g. resolution) are not used - Fix issue where non-default map coefficient parameters cause map names to be numbered - Fix issue where phenix.refine parameter diff could not be saved - Differences in DataManager PHIL are now included when using getting non-default parameters - Additional filtering is applied to Miller array selections to avoid ambiguity - The const_shrink_donor_acceptor default has been changed from 0.6 to 0.0 Please note that 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 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) 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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phenix quantum interface with Orca
by Guenter Fritz 30 Aug '24

30 Aug '24

Dear Phenix developers, I am currently trying the quantum interface on several cases. on https://phenix-online.org/documentation/reference/quantum_interface.html you write that one can also implement Orca. I am a very basic (not really experienced) Orca user, but nevertheless I would be happy to try it, since I have Orca installed on my , Ubuntu or Rocky) Is there a phenix variable that I have to point to Orca or can I set usage of orca in the .phil file with the package item? Thanks a lot and best regards, Guenter

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problem launching Phenix 1.21.1-5286 under Debian 12 Linux
by cparthier＠googlemail.com 29 Aug '24

29 Aug '24

Hi, I'm having problems running the current Phenix release (1.21.1-5286, but also earlier versions) on a fresh setup of Debian GNU/Linux 12 (bookworm, kernel 6.1.0-23-amd64). Phenix binaries have been installed on an NFS share ("hd1"), hostname is "phe". This is the error output: ----------------------------- phe:~> source /hd1/SOFT64/phenix-1.21.1-5286/phenix_env.csh phe:~> phenix Gtk-Message: 13:29:49.433: Failed to load module "canberra-gtk-module" Error in sys.excepthook: Traceback (most recent call last): File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/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 "/nfs/hd1/SOFT64/phenix-1.21.1-5286/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/nfs/hd1/SOFT64/phenix-1.21.1-5286/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) -------------------- Phenix does not run. The ""canberra-gtk-module" was missing first, but installing it did not prevent the error. Any hint what could be wrong? Thanks, Christoph

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Haskris R175 chiller available
by Jonathan Ruprecht 23 Aug '24

23 Aug '24

Dear bulletin board members, The MRC Mitochondrial Biology Unit in Cambridge, UK, has a Haskris R175-FEI-BHKL(RS) 3.2kVA air-cooled recirculating chiller (with hot gas bypass) that is now surplus to our requirements and available free of charge (the new owner would be asked to pay for transport). This was previously used to supply chilled water to a TEM. Please direct any enquiries to David Pate, MBU Laboratory Manager, ddp10(a)cam.ac.uk. Best wishes, Jonathan Ruprecht -- Dr Jonathan Ruprecht MRC Mitochondrial Biology Unit University of Cambridge Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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Presence of negative density in Sim Omit map
by Renuka Kadirvelraj 12 Aug '24

12 Aug '24

Presence of negative density in Sim Omit map Hi Phenixbb, We would appreciate your advice regarding an odd problem that has cropped up with one of our crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine residue in a loop, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, colored green in attached pics). However, flanking the positive density, there is a complimentary negative density (in red). We are puzzled as to the cause of the appearance of the negative density. Can you help us? Many thanks, Renu --------------------------------------------- Renu Kadirvelraj, Ph.D. Research Scientist A428, Biochemistry and Molecular Biology 120, East Green Street University of Georgia Athens, GA 30602 Tel: (706) 583 0303

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Maatel HC1c humidity controller available
by Jonathan Ruprecht 07 Aug '24

07 Aug '24

Dear bulletin board members, The MRC Mitochondrial Biology Unit in Cambridge, UK, has a Maatel HC1c humidity controller, together with the ancilliary components necessary to make a crystal dehydration rig, including a Nikon SMZ800 microscope, that is now surplus to our requirements and available free of charge (the new owner would be asked to pay for shipping). This was purchased in 2010, last used in approximately 2017 and is thought to be a working system. Please direct any enquiries to David Pate, MBU Laboratory Manager, ddp10(a)cam.ac.uk. Best wishes, Jonathan Ruprecht -- Dr Jonathan Ruprecht MRC Mitochondrial Biology Unit University of Cambridge Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb
by Alejandro Buschiazzo 02 Aug '24

02 Aug '24

Dear phenix users/developers Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc) Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties: 1- what’s the difference between miller_array and default_miller_array; or model and default_model? 2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff? 3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...) 4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files) Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!) Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop) With best wishes Alejandro

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