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PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
by Bjørn Panyella Pedersen 13 Jul '20

13 Jul '20

Dear colleagues, We have a open PhD position my my group. Please pass along to anyone who might be interested. Thanks! Deadline is July 31st. /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Deadline is July 31st. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk).

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phenix writing files with wrong job number
by Green, Todd Jason 09 Jul '20

09 Jul '20

Hello All- Phenix has started to write files from each job with incorrect job number notation. It puts them into the correct directory (ie. with correct job number, ex. Refine_23) but with file names having wrong job number (ie. where they are job number - 1, ex. protein_refine_22.pdb). This causes issues with the gui. I can edit the names post run, but is there a permanent fix. Just start a new project? Probably upgrade to the new version is the first choice. FYI I'm running 1.17.1-3660-000 on a macbook. Seems to have just started spontaneously. Thanks for the help- Todd

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The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine
by Zixian Li 08 Jul '20

08 Jul '20

Dear Phenix Community, I'm at beginner level of using Phenix. I have difficulty to refine a protein-RNA complex in Phenix. I refined the protein model without RNA first, then I built the RNA model into the difference density map in Coot through Calculate>Other Modelling Tools>Ideal DNA/RNA, where I input the sequence and fit nucleotides into the density. At the 5' end it's guanosine triphosphate (GTP) but the modeler tool in Coot only generates nucleoside monophosphate. So I built the RNA model from the second nucleotide at 5' end downstream until where RNA density was too poor to model. I did the real space refine zone in Coot to fit this main part of the RNA into its density the best possibly. For the GTP at 5' end, I realized there is GTP.cif restraint file in Phenix monomer library. So I obtained an arbitrary pdb file for GTP using eLBOW and corrected atom names matching the definition in GTP.cif file. Then I can also fit GTP into the RNA density at 5' end using real space refine zone in Coot. Now I have a broken RNA model with GTP unlinked to the ribose-phosphate backbone. For Phenix refinement, I supplied a cif_link_GTP-G.params file to define the linkage for the two RNA chains in the complex: refinement.pdb_interpretation { apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } } After refinement, I noticed O3' of GTP appears connected to P of the following nucleotide G in the refined model in Coot. However, if I do the real space refine zone in Coot, the linkage becomes broken, i.e., I cannot refine the RNA model as a whole: Coot only allows separate real space refine for GTP and the rest. It seems Coot still cannot recognize GTP and the rest as one body. In the refinement settings there is a button for Automatic linking options. Interestingly, I noticed if I leave the automatic covalent linking as default, Phenix writes Link records in the output pdb after refinement. But it also links one of the protein residues to the GTP in chain D. In order to avoid the unwanted intermolecular linkage, I clicked Link none for Automatic linking options, then there is no any link records written in the output pdb despite of the defined linkage in cif_link_GTP-G.params file. So it seems for me Phenix ignores the input cif_link_GTP-G.params file, it writes Link records only if the Automatic linking option is activated. I worried whether it could be due to the syntax of the cif_link_GTP-G.params file. So I tried the following syntax in two separate files, the same issue was observed. cif_link_GTP-G_chC.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } cif_link_GTP-G_chD.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } I also need to point out that p linkage is pre-defined in the list of links (mon_lib_list.cif) in Phenix monomer library. I apologize for this long explanation of the problem. I hope it is clear. I really appreciate your advice in advance. Sincerely, Zixian Li

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Heteroatoms addition to crystal structures
by Shirin Akbar 06 Jul '20

06 Jul '20

Dear all, I am using the phenix.real_space_refine program for refinement of crystal structure in cryo-EM map (ribosome map, 3.4 A resolution). Prior to real_space_refinement I had removed all the heteroatoms. What is the correct way to add the cations (eg. Mg2+ ions) to the structure and how do I do it? Can anyone kindly suggest.. Thanks & Regards Shirin -- *Shirin Akbar*

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real-space refinement resolution
by Alexei Gorelik 30 Jun '20

30 Jun '20

Hi, When refining a model against a density-modified cryo-EM map, should one use the resolution of the original or modified map? Thanks

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Refining cytochrome structure with hemes
by Yangqi Gu 30 Jun '20

30 Jun '20

Dear Phenix developers. I have a simple question regarding the real space refinement. I am working on a cytochrome structure and I would like to know how to refine the model with hemes present against the map? Also, how do I create vinyl bonds at my cysteine positions to connect the hemes? More ideally, could I refine the heme geometry as well? Thank you in advance! Best, Yangqi

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CryoEM Post-Doctoral Position
by Hasan, Syed Saif 25 Jun '20

25 Jun '20

Interested in exploring the world of molecular espionage? Want to find out how viruses hitchhike between organelles during assembly? Join my lab as a post-doctoral researcher to decipher the secret life of epidemic causing viruses at the atomic scale. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses such as Dengue, SARS-CoV-2, and pox viruses take over host membranes during intra-cellular progeny assembly. We are located in Rockville MD in the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan), which is 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 keV Talos Arctica with a Falcon 3EC DED and a 200 keV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. If you are interested, send me your CV. Lets talk. ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Energy minimization and explicit solvent model
by Andre LB Ambrosio 24 Jun '20

24 Jun '20

Dear colleagues, could you please suggest a computational tool to perform energy minimization of a crystal structure under explicit solvent conditions (i.e, types and concentrations of ions, pH)? I want to observe the solvent effects on the conformational space around a starting model, all-atom, while preserving its geometry (I guess it can be better expressed as relaxation). Thank you in advance. -- Andre LB Ambrosio

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Senior Scientist Position at AbbVie
by Jain, Rinku 24 Jun '20

24 Jun '20

Hi Everyone, I would like to draw your attention to the following job opportunity at AbbVie: Senior Scientist I, Protein X-ray Crystallography https://careers.abbvie.com/abbvie/jobs/2004610?lang=en-us&previousLocale=en… The Protein Crystallography Group at AbbVie (Illinois, USA) 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 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. AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. To learn more about AbbVie, please visit: https://www.abbvie.com/ Best, Rinku --------------------------------------------------------------------------------------------------------------------------------------------------- Rinku Jain, Ph.D. Senior Scientist II, Structural Biology [cid:[email protected]] I AbbVie, Inc. 1N. Waukegan Road, AP10-LL North Chicago, IL 60064-6098 EMAIL rinku.jain(a)abbvie.com<mailto:[email protected]>

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13th CCP4/APS Crystallographic School in the US
by Xu, Qingping 24 Jun '20

24 Jun '20

Dear Colleagues, We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php. Dates: June 15 through 22, 2020 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1th, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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