- phenixbb - phenix-online.org

AutoSol invalid MTZ column_types error
by Stan Yoo 19 Jan '17

19 Jan '17

Hello, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to do AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks

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phaser.labin not respected
by Murpholino Peligro 19 Jan '17

19 Jan '17

When I do in the terminal: phenix.phaser phaser.hklin="out.mtz" phaser.labin="F(+),SIGF(+),F(-),SIGF(-),merged" phaser.model="prot.pdb" phaser.mol_weight=14400 phaser.model_rmsd=0.3 my log file says it is using F and SIGF: LABIN F = F SIGF = SIGF Why it does not respect the labels provided? or..Am I doing something wrong. PS MR is successful Thanks

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help with Histidine flip in phenix refinement
by Vikram Dalal 19 Jan '17

19 Jan '17

Hi all, I have 4 Mn (2 Mn in each chain) in my protein structure. One Mn has 1 cordination with water, 1 cordination with His and 4 cordination with Asp. I model build the His in coot. Even this His is in bond range with Mn. But, when i refine this model in phenix. This His again flip other side (N terminal which has to cordinate with Mn goes to other direction). I am facing this problem only with His of A chain only while N of His of B chain are towards Mn only. Is there any option in pehnix refinment where we can exclude a specific residue or atom in refinment??

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Phenix.refine Restraints: replicating refmac external restaints
by Elliot Nelson 19 Jan '17

19 Jan '17

Hi All, Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e: Equivalent of: exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1 would be : refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } } If this is incorrect: Am i missing another way to create external restraint functionality in phenix, or am I making a more fundamental misunderstanding of how restraints are handled in both programs? Thanks in advance Elliot Nelson

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QuantumBio Release: XModeScore & DivCon Discovery Suite v7.1
by Lance Westerhoff 16 Jan '17

16 Jan '17

Hello All- I trust everyone had a nice holiday break and a Happy New Year! Today, we are excited to kick the new year off with a new release of our QM/MM refinement and analysis plugin for the Phenix platform. The full announcement, along with links to the details and licensing information, is available at this URL: http://www.quantumbioinc.com/news/show/DDS-012017 Thanks to our many users - academic, industrial, and government - who have provided feedback and support for this effort. This plugin, available within the DivCon Discovery Suite version 7.1, has a number of significant improvements applicable to users of Phenix including: * QM/MM X-ray Refinement Standard: Version 7.1 represents a complete overhaul of our MM and QM/MM implementation for improved stability, performance, and usability. Our fully automated QM/MM implementation has now come out of "beta" status and it is ready for production use. The implementation also supports truncated residues, multiple regions, and integrated ligand atom typing. * Application: Fragment Based Drug Design: Phenix/DivCon coupled with the novel, our patent pending XModeScore tool has been applied to several key areas including protomer/tautomer determination, binding mode selection, crystal water positioning, and now even fragment-based screening. We have provided a tutorial of MOE-based fragment docking coupled with XModeScore-based selection. * New Structure/Chemistry Analyses: The question we often hear from new users is how one can evaluate the performance of QM and QM/MM X-ray refinement vs. more conventional methods. We have now packaged several before/after analyses within refinement including Clash Scores (using phenix.molprobity); Strain, Interaction Energies, and ZDD (using DivCon); and GBVI/WSA dG binding score prediction (using MOE - as available). * New Feature [beta] - Protonation: Fast, integrated protonation and hydrogen bond network optimization is a perpetual problem in the field (especially in X-ray crystallography). This method uses a combination of dead end elimination and graph theory along with crystallographic symmetry and density - as available - to quickly and accurately determine the correct protonation states of bound ligands, active sites, waters, and protein/DNA/RNA. If you are interested in using or evaluating our linear scaling, quantum mechanics software in your drug discovery efforts or if you would like to schedule an on-line or on-site meeting to discuss the technology, please email sales(a)quantumbioinc.com and let us know. And as with last year, we are waiving the license free for non-profit, academic users as per academic license agreement. Our academic, commercial, consulting, and evaluation licenses are available on-line (most for electronic signature): http://www.quantumbioinc.com/products/software_licensing Have a great 2017! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

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Berkeley Server Downtime (1/13 - 1/14)
by Billy Poon 15 Jan '17

15 Jan '17

Dear all, On Friday, January 13, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (1/14) by 6:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Calculation of bond lengths, angles and torsion angle for large number of proteins
by Ashraya Ravikumar 11 Jan '17

11 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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Postdoctoral Fellow Position at US MHRP, WRAIR
by gjoyce＠hivresearch.org 29 Dec '16

29 Dec '16

Dear All, A postdoc position is available in a newly formed Structural Biology Section, part of the US Military HIV Research Program, WRAIR in Silver Spring, Maryland, USA. The position involves the application of structural biology to understanding viral glycoproteins and the immune response following vaccination or natural infection. Interested and qualified individuals can apply through the following official link at Job ID: 212324 at the Henry M Jackson Foundation careers website: http://www.hjf.org/careers/open-jobs. Applicants must be US citizens or have lived in the US for at least 3 consecutive years. Please feel free to contact me at gjoyce(a)hivresearch.org if you have any questions. Best wishes, Gordon HJF is seeking a Postdoctoral Fellow to support the Military HIV Research Program (MHRP) located at the Walter Reed Army Institute of Research (WRAIR) in Silver Spring, Maryland. The incumbent will be responsible for initiating and carrying out scientific projects, under the supervision of senior scientists and in collaboration with other research scientists. The position involves the characterization of the humoral immune response to HIV-1 infection and HIV-1 vaccines using X-ray crystallography. The incumbent will be responsible for conducting and publishing research in HIV structural biology. The incumbent will work within a multidisciplinary environment consisting of military, government, academic, and international collaborators. Responsibilities: Conducts independent research and learns techniques required to conduct the research. Assists in designing, developing, executing, and implementing scientific research and/or products. Develops a thorough understanding of the scientific literature relating to the research topics. Collects and handles samples and keeps detailed inventory and records of experiments by maintaining up to date, clear, and accurate laboratory notebooks. Executes projects related to biochemical and structural characterization of antibodies, vaccine candidates and their complexes. Analyzes experimental data, applying relevant statistical and bioinformatic models. Presents data at scientific meetings and publishes original research in peer-reviewed journals. Assists with training laboratory staff and collaborates with labs within and outside of MHRP. Follows all MHRP and WRAIR safety procedures and completes required training in a timely manner. Performs other duties as assigned. Required Knowledge, Skills, and Abilities: PhD in structural biology or related area with significant experience in X-ray protein crystallography. Knowledge of appropriate scientific area; ability to analyze and interpret data. Experience and proficiency in protein purification, protein characterization, X-ray crystallography including up-to-date knowledge of relevant programs including CCP4, and Phenix packages. Experience with project planning, implementation, and data analysis. Experience in presenting at scientific meetings and writing manuscripts for scientific journals. Practical knowledge of electron microscopy, molecular modelling or structure-based mutagenesis and design is an advantage. Minimum Education/Training Requirements: Ph.D. in structural biology, molecular biology, immunology, microbiology, biochemistry or related discipline. Minimum Experience: 0-2 years of postdoctoral experience Physical Capabilities: Long periods of standing and sitting; intricate work with hands; carrying of light and moderately heavy laboratory equipment. Job performance requires movement around and between several laboratories, and long periods of sitting at laboratory bench. Fine motor coordination in manipulation of laboratory materials is essential. Supervisory Responsibilities/Controls: May provide guidance to laboratory staff. Work Environment: Laboratory environment; may require working evenings and weekends. The incumbent will be expected to practice safe handling of hazardous chemicals. This laboratory is densely populated and requires good interpersonal skills for effective job performance. This position requires working and occasional travel to US synchrotron facilities. This Postdoctoral Fellow will support the US Military HIV Research Program, located at The Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. HJF is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or protected veteran status. Any qualifications to be considered as equivalents, in lieu of stated minimums, require the prior approval of the Director of Human Resources. M. Gordon Joyce, Ph.D. Chief, Structural Biology Section The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 gjoyce(a)hivresearch.org Web: www.hivresearch.org Facebook: www.facebook.com/hivresearch YouTube: www.youtube.com/mhrpvideos Twitter: www.twitter.com/mhrpinfo The U.S. Military HIV Research Program (MHRP), centered at the Walter Reed Army Institute of Research (WRAIR), is an international HIV vaccine research program that successfully integrates HIV/AIDS prevention, care and treatment.

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Spring 2016 MicroED workshops at Janelia Research Campus
by Hattne, Johan 22 Dec '16

22 Dec '16

Due to high demand, two back-to-back MicroED workshops will be held at Janelia Research Campus (Ashburn, VA) in the spring. The workshops are hosted by Tamir Gonen and will have the same content. Accepted participants will be assigned by the organizers to one or the other (not both). May 21-24 and May 24-27, 2017 MicroED is a cryoEM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryoTEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To facilitate the widespread use of MicroED, we are offering these workshops to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Applicants must register and submit a brief statement on why they wish to participate, via our online registration system. https://conference.janelia.org Please note that this system is designed to collect abstract information for presentations. Please write your statement of interest in the "abstract" field, put your name in the "author" field, and put "n/a" in the "presentation title" and "keyword" fields. Space in these workshops is limited. The application deadline is February 10, 2017. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Job opportunity - Structural Biology GSK Vaccines
by Enrico Malito 22 Dec '16

22 Dec '16

Dear phenix community, The Structural Biology Lab at GSK Vaccines, Rockville, MD, USA, is seeking a candidate for a Scientist/Senior Scientist position (Job ID: 148543, hiring managers: Enrico Malito, Matthew Bottomley). We offer outstanding opportunities and compensation to outstanding candidates. Anyone interested to apply can do so by visiting this link: https://careers.peopleclick. com/careerscp/client_gsk/external1931/en-us/gateway.do? functionName=viewFromLink&jobPostId=323652&localeCode=en-us (Please note that this may wrap to another line of text; you may need to copy and paste the entire URL into your browser window). Applications will be accepted only through the page at the link above. Examples of relevant recent publications: - Rappuoli et al 2016. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. http://dx.doi.org/10.1084/jem.20151960 - Chandramouli et al 2015. Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody http://dx.doi.org/10.1038/ncomms9176 - Ciferri et al 2015. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies http://dx.doi.org/10.1371/journal.ppat.1005230 - Malito et al 2015. Protein Crystallography in Vaccine Research and Development. http://dx.doi.org/10.3390/ijms160613106 Yours sincerely, *Enrico Malito, PhD* *Lab Head of Structural Biology and BiophysicsGSK VaccinesPreclinical R&D USGSK Vaccines14200 Shady Grove Road, Rockville MD 20850, USA*

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alingments in mr_rosetta
by Kajander, Tommi A 21 Dec '16

21 Dec '16

Hi, I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it? also the command file examples online e.g. : phenix.mr_rosetta \ seq_file=seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ already_placed=True \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=2 \ space_group=p212121 \ use_all_plausible_sg=False \ nproc=200 \ group_run_command=qsub when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial. -if i just enter them on the command line it works. Thanks, Tommi

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Error from f_model_all_scales.py
by John Bruning 19 Dec '16

19 Dec '16

Hi (Pavel), I have a dataset (P31) which I am processing with the pairwise combinations of reindexing operators (4 incl. no reindexing therefore h,k,l) and twin laws (4 incl. no twinning as h,k,l). While some of these combinations are fine during refinement (Vers 1.11.1), for some combinations I get the following error, which ultimately kills the refinement. Thanks in advance and apologies if I am missing something stupid. Incidentally, a different dataset seems to tolerate all combinations. *approx_equal eps: 1e-05* *approx_equal multiplier: 10000000000.0* *0.512707954357 approx_equal ERROR* *0.514972857238 approx_equal ERROR* Traceback (most recent call last): File "/Applications/phenix-1.11.1-2575/build/../modules/phenix/ phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/command_line.py", line 154, in run call_back_handler=call_back_handler) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/driver.py", line 1529, in run call_back_handler = call_back_handler).result File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/strategies.py", line 121, in __init__ log = log) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/fmodels.py", line 159, in run fmodel.update_solvent_and_scale(initialise=True) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/twinning/twin_f_model.py", line 797, in update_solvent_and_scale params=params, log=log, apply_back_trace=apply_back_trace) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1457, in update_all_scales params = params, log = log, refine_hd_scattering=refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 38, in __init__ refine_hd_scattering = refine_hd_scattering, log = log) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 61, in compute refine_hd_scattering = refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 329, in update_solvent_and_scale_twin * assert approx_equal(self.r_all(), o_kbu_sol.r(), 1.e-5)* *AssertionError*

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phenix rosetta interface
by CPMAS Chen 16 Dec '16

16 Dec '16

Hi, All, When I compile phenix-1.11-2567 and rosetta-bin-mac_2016.37.58930_bundle interface, I got the following error message. Any suggestion to fix this? Thanks! src/core/scoring/cryst/PhenixInterface.cc:253:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( pdbout , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ src/core/scoring/cryst/PhenixInterface.cc:916:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( buffer , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ 2 errors generated. scons: *** [build/src/release/macos/16.1/64/x86/clang/8.0/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Asymmetric unit content
by Sharan Karade 12 Dec '16

12 Dec '16

Dear all, I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide. advance thanks for valuable suggestions. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Recent improvements in Phaser for systematically weak data
by Randy Read 09 Dec '16

09 Dec '16

Dear all, Between the last official release of Phenix (version 1.11.1-2575, released on 26 October) and a recent CCP4 update (7.0.023 released on 23 November), we fixed a problem in which the fast rotation function was not properly accounting for the effect of measurement errors in intensities. Under many circumstances (i.e. with well-measured data to the resolution needed to solve the structure by MR), the change is not noticeable. However, if you have systematically weak data (particularly from high levels of anisotropy or potentially from the effects of translational non-crystallographic symmetry), the fix can mean the difference between failing to solve the structure, because the correct orientation has not been generated, or solving it with a default run of Phaser. We recommend that anyone trying to solve a structure with substantial anisotropy (anisotropic deltaB of 50 A^2 or greater) and/or translational NCS should update to a newer version of either package. If you're using CCP4, you should get the latest update, because there was a problem with the version of coot distributed with the 7.0.023 update. If you're using Phenix, you should get a recent nightly build, i.e. dev-2608 or something even newer. Please note that you want to provide data to Phaser in the form of intensities rather than amplitudes to get the best results for such data! So far, I've found 3 of our test cases where this makes a real difference, but I would be interested in hearing from anyone who finds that this makes a difference for other cases. Best wishes, Randy Read ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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iNEXT access: NMR Extended Support and more!
by Anastassis Perrakis 06 Dec '16

06 Dec '16

Dear all, I should perhaps offer sincere apologies for posting the crystallography boards with NMR news ;-). However, I will not do that, as I sincerely hope you will see that in an era of integration of structural methods, such opportunities can offer the chance for excellent and exciting scientific endeavours. iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) is committed to bring structural methods closer to non-experts, by funding access to world class infrastructures for Structural Biology. Major tools for achieving that goal are the so-called Extended Support modalities. We are happy to announce the start for acess to the iNEXT Enhanced Support modality for NMR (NMR assignment, structure, dynamics). In this mode, the NMR groups in Florence, Frankfurt and Utrecht are involved in guiding and training NMR novices. This iNEXT access modality also targets "new users with backgrounds other than Structural Biology”, so please feel free to forward that also to your biochemistry friends. Facility personnel will be involved to guide assignments, titrations, structure calculations, relaxation analyses, etc. I also want to bring your attention to a few more iNEXT news: - The Structural Audit, now allows multiple samples in a related project to be submitted in a single application for stability assessment and crystallisation screening; a basic analysis by SAXS, EM, or NMR is also supported (single click in application!) if an appropriate sample is available. - The Enhanced Support modality "From macromolecular sample to X-ray data collection” is now better integrated with Structural Audit; applications can be combined, so in case of a successful Audit, you could rapidly proceed to further X-ray experiments (crystal optimisation, SAXS and/or crystallography) - The Enhanced Support modality "Advanced light imaging” to support structural studies with in cells measurement of protein interaction kinetics, have also been made recently available. - The Enhanced Support modality "Cryo-EM sample optimisation” for hands-on assistance in optimizing a sample for single particle EM is a great chance to move your sample towards cryo-EM! - The Enhanced Support modality "Macromolecular interactions” is your chance for access to a Biophysics facility with various instruments and hands-on support for performing and analysing experiments to quantify a variety of interactions. - All the High-End modalities (X-rays, NMR, cryo-EM) are always open for access! So, please, submit your proposal now! <https://www.structuralbiology.eu/update/submit-proposal?t=inext> … and keep in mind that a limited amount of the funding (~10%) can go towards projects that are not in an EU-country or associated country. On behalf of the iNEXT Management, Best wishes, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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