- phenixbb - phenix-online.org

Isolate Protofilament from helical reconstruction
by Christian Tüting 09 Nov '22

09 Nov '22

Dear PHENIX mailing list, I have a question regarding a helical reconstruction, done in cryoSPARC. Usually, I work with "normal" symmetric particles, and there I can simply run phenix.map_box to isolate the asymmetric unit. This is somehow not possible with a helical map. As we also don't have an atomic model yet, we cannot just crop it with map_box. In our helical reconstruction, we have helical twist (in degree) and the helical rise (in Å) and a additional point group symmetry. We would like to isolate a single protofilament for further model building. Is this in principle possible in PHENIX? Additionally, is there a way to rebuild the helical structure, analogous to apply_ncs? Thanks Christian

2 1

Douse adding waters with overlapping residue number
by Adrián González López 02 Nov '22

02 Nov '22

Dear phenix developers, When I run phenix.douse it assigns the waters to the closest chain, but it also attributes them the residue number 0, 1, 2, 3, 4…. which overlaps with the protein residues. Is this a bug? My workaround is to run phenix.sort_hetatms right after and it renumbers them correctly. I am on phenix version 1.20.1-4487-000 Thanks! 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

Scientist in Protein Crystallography -- ZoBio Leiden
by Misba Ahmad 31 Oct '22

31 Oct '22

ZoBio (www.zobio.com) was founded in 2004 and is located in Leiden, Netherlands. We offer innovative research services in the field of small-molecule drug discovery to the pharmaceutical and biotech industries. Our international team of 40 people covers five fields of expertise: Protein Sciences, Assay Development and Screening, Structural Biology, Medicinal Chemistry, and Data and Information Sciences. We are looking to strengthen our Structural Biology team with an enthusiastic scientist with a track record in protein X-ray crystallography. The structural biology team plays a critical role in supporting our clients’ drug discovery programs by providing structural insights into protein-ligand complexes by both NMR spectroscopy and X-ray crystallography. Our crystallization laboratory is equipped with state-of-the-art liquid handlers and automated imagers, and we have regular access to the main European synchrotrons. The team is involved in many projects with challenging targets and engaged in exploring innovative workflows. It is fully expected that the successful candidate will become a permanent and integral member of the ZoBio team after an initial 12-month contract. A tailored remuneration package will be proposed in line with individual qualifications and experience. The position is immediately available; the evaluation and assessment of candidates will run until the position is filled. *TASKS & RESPONSIBILITIES* As a member of the Structural Biology group, you will work on site in the laboratory primarily to support crystallization and structure determination of protein-ligand complexes. You will work with minimal supervision but in a highly collaborative environment within the Structural Biology group and will effectively cooperate on a per-project basis with other research groups at ZoBio. Your role will require working simultaneously on multiple projects in a rapidly evolving environment. You will: Provide input to research projects: - Design and implement (co-) crystallization and soaking strategies utilizing automation and robotics - High-throughput and -quality structure elucidation and interpretation of biological macromolecules in complexes with small molecules of interest - Troubleshoot proactively various challenges relating to protein crystallization - Perform experiments with deadlines - Report project results in an accurate and concise manner, both verbally and written - Keep up to date with relevant literatures and developments in the field of protein crystallography Organize logistics, planning and quality control for research projects: - Contribute to the overall quality control process of data that is generated by the group members - Control the integrity of data imported in project databases - Develop innovative approaches to protein crystallization and/or structure determination, including evaluation of new technologies that support and improve the workflow - Share knowledge, observations, and insights within the group and ZoBio to improve quality and efficiency of project proceedings - Collaborate with clients, external CROs and suppliers *PROFILE & COMPETENCIES* The ideal candidate has a strong background in biochemistry, biophysics or structural biology and at least 4 years of hands-on experience in protein crystallization and structure determination using standard crystallization software (e.g., CCP4, Phenix). Hands-on experience with crystallization robots and understanding of molecular interactions in the context of ligand modelling is desirable; a willingness to learn is required. The multitude of ongoing projects in a rapidly changing environment demands a flexible, creative, and highly organized person with hands-on mentality and excellent communication skills. Required competencies include: - Problem analysis: ability to identify problems, recognize important information, make connections between data, and trace possible causes of problems - Creativity: ability to come up with original solutions, and think ‘out-of-the-box’ to design novel strategies - Work standards: setting high quality standards with respect to performance of experiments and data analysis, and act accordingly - Oral and written communication: ability to communicate in a clear, persuasive, and effective way to colleagues and clients about ideas, and to report project progress in an accurate and reproducible manner - Adaptability: ability to adjust one’s behavior, planning, and organization in response to frequent changes, delays, and unexpected events - Teamwork: ability to contribute actively to a joint result or solution, even when such teamwork concerns a matter which is not of immediate personal interest - Tenacity: ability to stay with a plan of action or point of view until the desired goal has been attained or is no longer reasonably attainable - Planning and organization: ability to plan and organize tasks and projects to meet the defined goals Please send your CV, motivation letter and names of potential referees to < hrm(a)zobio.com*>* with the subject: “Scientist in Protein Crystallography”.

1 0

staff scientist position for an experienced protein crystallographer
by Mooers, Blaine H.M. (HSC) 28 Oct '22

28 Oct '22

The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Staff Scientist level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography, a strong work ethic, and the ability to independently carry out each step of the standard crystallographic study workflow: this a service position, not a training position. The candidate will not be expected to write grant applications to support their position. Pluses in a candidate's background include experience with instrument repair, eukaryotic protein expression, membrane protein purification and LCP crystallization, Cyro-EM, microED, SAXS, SANS, XAFS, NMR, or XFELS. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The OCSB was awarded five more years of NIH funding in May 2022. The BSC has contributed to the awarding of 26 million dollars in grant funding and 36 publications in the past ten years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC is a vital part of a new Center for Therapeutic Science. The center coordinates and fosters the drug development pipeline with the BSC playing a central role in structure-based drug design. The LBSF is working closely with Dr. Matt Hart (https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1), Director of the newly established Center for High Throughput Screening. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer (https://pubmed.ncbi.nlm.nih.gov/33161056/). Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at ouhsc.edu. Also apply for Job # 223015 – Staff Scientist Structural Biology at jobs.ou.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

1 0

Bond angle outliers missing from the list
by Adrián González López 22 Oct '22

22 Oct '22

Hi! I performed a real space refinement on my EM map and my validation summary indicates that I have 17 bond angle outliers. However, when I check on the MolProbity tab, Geometry Restraints, it only shows me one of them (and it still says there are 17). Is this a bug or something else? You can see it on the screenshot below: [cid:BADACC33-3B23-4F5B-8847-E5C39FCB01F3] Thanks! /Adrian 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

3 2

geometry minimization with ligand present
by CPMAS Chen 21 Oct '22

21 Oct '22

Hi, All, I have a structure calculated with NMR restraints but it has quite some geometry violation, such as torsion angles, clashes etc. The structure has a small molecule ligand bound. Is it possible to add an CIF file for the ligand and use phenix.geometry_minimization to idealize/optimize the protein structure? I have tried the following and phenix reported an error for missing CIF file. phenix.geometry_minimization model.pdb pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif what would be the correct syntax to add ligand cif for this geometry_minimization? Or what would be the proper way to idealize/optimize a protein structure with ligands present? The structure optimization during NMR calculation is not good enough in my case. Thanks! Charles *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

2 3

Re: [phenixbb] 3rd CCP4/BGU Workshop on Data Collection and Structure Determination
by Anat Shahar 14 Oct '22

14 Oct '22

Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including “how to apply”, registration form and tentative program, can be found at: https://lifewp.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2022. Best wishes, Anat Shahar & Eugene Krissinel

1 0

Re: [phenixbb] 3rd CCP4/BGU Workshop on Data Collection and Structure Determination
by Anat Shahar 14 Oct '22

14 Oct '22

Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including “how to apply”, registration form and tentative program, can be found at: https://lifewp.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2022. Best wishes, Anat Shahar & Eugene Krissinel

1 0

3rd CCP4/BGU Workshop on Data Collection and Structure Determination
by Anat Shahar 14 Oct '22

14 Oct '22

Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including “how to apply”, registration form and tentative program, can be found at: https://lifeserv.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2023. Best wishes, Anat Shahar & Eugene Krissinel

1 0

X-ray crystallography software developer position at Astex
by Gabor Bunkoczi 09 Oct '22

09 Oct '22

Dear All, We have an opening for a skilled software developer with crystallographic computing background at our Cambridge (UK) site. For more information about the position, please see the full advert: https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSear… To apply, please follow the link in the advert. For informal enquiries, please feel free to contact me. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

1 0