- phenixbb - phenix-online.org

Calculation of bond lengths, angles and torsion angle for large number of proteins
by Ashraya Ravikumar 12 Jan '17

12 Jan '17

Hi All, I would like to calculate all the bond lengths, bond angles and main chain torsion angles for a large set of proteins, in PDB format. Could you please let me know which module/command in phenix is suitable for this task? Regards, Ashraya

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Re: [phenixbb] Modified DNA residue
by Pavel Afonine 11 Jan '17

11 Jan '17

Hi Melissa, we need to have a closer look to understand what's happening... Could you please send us these PDB file: - original (before modifications); - file after modifications; - file after refinement; - cif file. Pavel On 1/11/17 14:15, Melissa Ford wrote: > I'm having working on modeling a sulfur on the phosphate backbone of > DNA in replace of one of the oxygens and have encountered some > restraint problems. I've successfully managed to replace the oxygen > with a sulfur in the proper geometry in a pdb, generate a cif file for > the modified residue (adenosine 5'-phosphorothioate), and run an > initial refinement. Upon that refinement, a few errors occur. First, > since the phosphate bound to the sulfur is the first atom of the > modified residue the angle between the O3' (of the neighboring > residue) - P- S is not recognized and forced into an unfavorable > geometry. When trying to add that additional angle to the cif file, I > get an error. Aditionally, the change causes Phenix to not recognize > the chirality of the C3' that the phosphate is bonded to and forces > the ribose into a planar conformation. I am sure there is something I > am missing that allows phenix to recognize this new residue as a > modified nucleotide so that it knows these restraints. Any insight on > this would be great. Thank you!

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Modified DNA residue
by Melissa Ford 11 Jan '17

11 Jan '17

I'm having working on modeling a sulfur on the phosphate backbone of DNA in replace of one of the oxygens and have encountered some restraint problems. I've successfully managed to replace the oxygen with a sulfur in the proper geometry in a pdb, generate a cif file for the modified residue (adenosine 5'-phosphorothioate), and run an initial refinement. Upon that refinement, a few errors occur. First, since the phosphate bound to the sulfur is the first atom of the modified residue the angle between the O3' (of the neighboring residue) - P- S is not recognized and forced into an unfavorable geometry. When trying to add that additional angle to the cif file, I get an error. Aditionally, the change causes Phenix to not recognize the chirality of the C3' that the phosphate is bonded to and forces the ribose into a planar conformation. I am sure there is something I am missing that allows phenix to recognize this new residue as a modified nucleotide so that it knows these restraints. Any insight on this would be great. Thank you!

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error message after running phenix.refine: Unable to create Kinemagefile: float division by zero
by Georg Mlynek 11 Jan '17

11 Jan '17

Dear All, I getting this error message at the end of running phenix.refine: Unable to create Kinemagefile: float division by zero I just get this running phenix.refine on a neutron structure. Joint refinements are fine. I am using dev-2621 and ubuntu 15.10. Thanks in advance best regards, Georg.

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8th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 10 Jan '17

10 Jan '17

First announcement 8th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 5 - June 9, 2017 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/66/ Application deadline: April 22, 2017 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome - however the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2017. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Scientist position at AbbVie
by Longenecker, Kenton L 09 Jan '17

09 Jan '17

Hi - Please see the following job opportunity below and find full description to apply at: http://abbvie.taleo.net/careersection/jobdetail.ftl?job=1608252&lang=en Senior Scientist II, Structural Biology-1608252 AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 28,000 people worldwide and markets medicines in more than 170 countries. Description The Protein Crystallography Group at AbbVie Headquarters in Lake County, Illinois is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern X-ray Crystallography techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize fragment-based strategies to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Principal Scientist AbbVie R&D Discovery, DCAT Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Academic position in glycoscience at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

Not to be confused with our previous job posting - please note the earlier deadline (5th of February) for this one! The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in glycoscience with a clear vision to lead their own programme of excellent research, which will complement that of Professor Gideon Davies, FRS FMedSci and other members of the York Structural Biology Laboratory (YSBL). The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. We would particularly welcome applications from researchers with a track record in chemical biology approaches to mammalian glycoscience; preferably with biomedical aspects. You will join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key Requirements (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in a Chemical or Biochemical Science - Demonstrated expertise in a field/fields central to glycoscience - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297414 Deadline for applications: 05/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

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Academic position in cryoEM at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within the York Structural Biology Laboratory (YSBL). Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. You'll join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key requirements: (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo-electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journals - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297412 Deadline for applications: 12/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

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Multiple positions in Buffalo NY
by Edward Snell 05 Jan '17

05 Jan '17

Dear All, Just a reminder for those that may have missed it over the holidays. We have multiple positions for structural biologists in Buffalo NY. Please let anyone who may have an interest know of these opportunities. The first is with the Hauptman-Woodward Medical Research Institute: The Hauptman-Woodward Medical Research Institute (hwi.buffalo.edu) operates the High-Throughput Crystallization Screening Center providing crystallization and characterization services to the community at very competitive cost (www.getacrystal.org). A Ph.D. level research scientist position (post-doctoral or junior researcher) is available within the Center to guide operations on a daily basis, move research capabilities into production, and to help set the direction of the Center for the future. There is strong potential for both scientific growth and growth of responsibility. The candidate would be expected to have demonstrated expertise and productive research in the area along with appropriate publications. In addition to crystallization knowledge, experience with structural biology techniques in general is desired. Computational experience is a plus. The candidate should gave excellent communication, reading, writing, and presentation skills. They should be able to be a representative of the Center in the scientific community. They should have a good interpersonal skill set and be able to work with a diverse group. Evidence of seeking their own research funding would be viewed as a strong positive and the position would encourage the development of capabilities through active research efforts and collaboration. The Center interacts with both academia and industry and provides some crystallization screening services for a growing Gene to Structure company, HarkerBIO, (www. harkerbio.com). Collaborative possibilities are possible in this area. Research facilities at the Center include liquid handling robots, in-house developed plate imaging capabilities, SONICC and UV analysis, and X-ray analysis. The Center is well connected to several synchrotron facilities. A sophisticated computational infrastructure is in place. In both the X-ray and computational side, research advances are ready to be implemented into the Centers capabilities. The Hauptman-Woodward Medical Research Institute is 60 years old and based in Buffalo New York. It is at the center of a rapidly expanding medical campus. Good benefits are provided and the cost of living in the area is very competitive. For those with a focused research interest, the Institute is located adjacent to high-end computer facilities, a Comprehensive Cancer Center, a new Medical School under construction, and multiple biotech startup companies. Collaborative efforts with academic and industrial collaborators are strongly encouraged and aided by an umbrella organization on the campus. The Hauptman-Woodward Medical Research Institute, Inc. as an equal opportunity employer, extends employment opportunities to qualified applicants and employees on a non-discriminatory basis without regard to race, color, sex, creed, age, religion, national origin, marital status, veteran status, sexual orientation, genetic predisposition, carrier status, or disability that would prevent the performance of the essential requirements of the job with or without a reasonable accommodation in compliance with the appropriate New York State and Federal laws, or any other legally protected characteristics. This policy applies to all conditions and terms of employment. Formal applications should send a cover letter and resume along with three contacts for references to opportunity(a)hwi.buffalo.edu. The position is available in the New Year and will be open until filled. And on behalf of Artem Evdokimov, HarkerBIO CEO, the other positions are with a company called HarkerBIO housed in the Hauptman-Woodward Medical Research Institute building: HarkerBIO is hiring two *Research Scientist - Structural Biology * positions. Desired qualifications are quite broad, but can be summarized as follows: 1) someone who is a start-up enthusiast, not afraid of a challenge and has both the desire to innovate in science and the ability to do so. A PhD in related area is a plus, however we would consider qualified M.Sc. candidates. 2) someone with a relevant experience in at least 70% of the gene to structure 'process' - in other terms, the candidate is able to perform literature research, design clones, clone, express, purify, crystallize and solve structures -- or at least a good chunk of the above. Ideally someone with experience in mammalian and/or insect cell expression, and/or membrane protein work. 3) a scientist with a reasonably rounded skill set in biophysical characterization of macromolecules (SPR, DSF, anSEC/MALS, and so forth) 4) deep interest in developing structure-related technologies (e.g. expression systems, crystallization research, etc.). Desire and ability to participate in internal research projects. 5) high work ethic, impeccable documentation abilities, sense of humor 6) committed to relocating to Buffalo, NY HarkerBIO offer: Competitive salary (commensurate with experience) and full benefits Energetic and friendly work environment Coverage of reasonable relocation expenses for highly qualified candidates Co-location with a nonprofit research institute (HWI) and participation in the thriving research community at the Buffalo-Niagara Medical Campus HarkerBIO is an EO/AA employer. Please direct your inquiries to careers(a)harkerbio.com<mailto:[email protected]>. Note that for both positions, applications should be addressed to the emails given in the position descriptions. Happy New Year, Eddie Edward Snell Ph.D. President and CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.buffalo.edu Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu [cid:[email protected]] Heisenberg was probably here!

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Phenix.model_vs_data - Rfree difference
by Luca Pellegrini 02 Jan '17

02 Jan '17

Hello, I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data: phenix.refine R-work/R-free 0.1702/0.1974 phenix.model_vs_data R-work/R-free 0.1728/0.1795 Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy: phenix.refine R-work/R-free 0.1720/0.2086 phenix.model_vs_data R-work/R-free 0.1715/0.2080 Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine. Thanks for the help & happy New Year, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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