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Problem in real space
by Firdous Tarique 27 Jul '21

27 Jul '21

Hi I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out where. Can we do something in refinement settings Or change any threshold value to avoid these problems? Input is 80S.pdb ribosome and its corresponding em map. File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff raise RuntimeError(msg) Best regards Firdous

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post-doc position at KU Leuven, ligand-gated ion channels
by Chris Ulens 26 Jul '21

26 Jul '21

A post-doctoral position is available at the Laboratory of Prof. Chris Ulens, KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of Structural Neurobiology is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our methods rely on X-ray crystallography and cryo-EM in combination with electrophysiological recordings and fluorescence-based techniques. Our laboratory hosts an integrated macromolecular crystallization facility with a Mosquito crystallization robot and two RockImagers. We have access to a 200 kV Glacios microscope on campus as well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current projects are situated at the crossroads of structural elucidation and drug discovery of different pentameric ligand-gated ion channels. We would like to recruit a post-doc with prior experience in cryo-EM or X-ray crystallography of membrane proteins. The successful candidate: - easily communicates in an open verbal manner and has a team player spirit - has an ambitious work ethic - critically contributes to writing of manuscripts and grant proposals - makes efforts to obtain independent funding - meets intermediate deadlines and brings projects to a successful end - fuels internal discussions of recent publications in the field - sets an example to younger PhD students in the lab - identifies directions for future scientific research The position is open immediately and applications will be accepted until the position is filled. Applicants are requested to submit a CV with publication list and two references. E-mail to chris.ulens(a)kuleuven.be Selection of recent publications: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4. Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511. The structural basis for an on-off switch controlling Gβγ-mediated inhibition of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117.

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Move fem map back to protein?
by Murpholino Peligro 23 Jul '21

23 Jul '21

Dear all.. How do I move a fem map back to the protein molecule? I did `phenix.fem PHASER.1-coot-1_refine_001.pdb PHASER.1-coot-0_refine_data.mtz` to generate the fem map, but when I open with coot `coot PHASER.1-coot-1_refine_001.mtz PHASER.1-coot-1_refine_001.pdb` and then file->open map->fem.cpp4... the fem map does not cover the protein (as shown in .png attached) I am not sure if this is phenix (a missing option?) or coot related ... thanks

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Ligand Library
by Christian Tüting 23 Jul '21

23 Jul '21

Dear Phenix-Team, dear Mailing-List, I have a question regarding bound ligands during refinement. In our initial structure, we have multiple spheroidenes bound (pdb ligand id SPO), but experimental data suggest that it should be speroidenones (pdb ligand id SPN). The difference between these molecules are located in an additional oxygen at the head group and a different saturation level of the carbon chain. I mananged to exchange the molecule using Coot, but during refinement I got following error: Number of atoms with unknown nonbonded energy type symbols: 602 "HETATM18420 C1 SPN B 600 .*.N C " "HETATM18421 C10 SPN B 600 .*.N C " "HETATM18422 C11 SPN B 600 .*.N C " "HETATM18423 C12 SPN B 600 .*.N C " "HETATM18424 C13 SPN B 600 .*.N C " "HETATM18425 C14 SPN B 600 .*.N C " "HETATM18426 C15 SPN B 600 .*.N C " "HETATM18427 C16 SPN B 600 .*.N C " "HETATM18428 C17 SPN B 600 .*.N C " "HETATM18429 C18 SPN B 600 .*.N C " ... (remaining 592 not shown) So, as far as I understand this error, the ligand is not in the restrained in the ligand library. I followed this tutorial: https://phenix-online.org/documentation/tutorials/elbow.html to generate the .cif file for refinement. I was just using the pdb file and the geometry from there, as it was "coot-refined" and thereby I expected the correct conformation. The refinement than run fine, but the ligand after refinement is in a complete wrong conformation and parts of the carbon chain is outside the density. I am not sure, if this is due to low resolution at these regions (which are indeed very low compared to other ligands or proteins in the map), or if during restraining something went wrong. Is it possible to add this ligand to the phenix ligand library or do you have any suggestions, how to improve the restraining using the elbow tool? Thanks in advance Christian Tüting Dr. rer. nat. Christian Tüting Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Two positions (postdoc and PhD) in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 14 Jul '21

14 Jul '21

Dear all, Just a reminder that we have two open positions (1 postdoc and 1 PhD) available to join our team and investigate metabolite transport using structural biology. Please pass along to anyone who might be interested. Thanks! PhD position = https://bit.ly/3Ak5Far Postdoc position = https://bit.ly/2SXS7Rm /Bjørn ----------------------------------------------------------------------- STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD and a postdoc position are available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn 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 (see http://pedersenlab.dk). The projects will be developed in discussion with the selected candidates, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The projects are fully funded by the European Research Council (ERC). The candidates 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, but start date is negotiable. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university.

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geometry_minimization makes molprobity score worse
by James Holton 14 Jul '21

14 Jul '21

Greetings all, and I hope this little observation helps improve things somehow. I did not expect this result, but there it is. My MolProbity score goes from 0.7 to 1.9 after a run of phenix.geometry_minimization I started with an AMBER-minimized model (based on 1aho), and that got me my best MolProbity score so far (0.7). But, even with hydrogens and waters removed the geometry_minimization run increases the clashscore from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one residue reaching the outlier level. Just for comparison, with refmac5 in "refi type ideal" mode I see the MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from favored to allowed, but none rise to the level of outliers. Files and logs here: https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz I suspect this might have something to do with library values for main-chain bonds and angles? They do seem to vary between programs. Phenix having the shortest CA-CA distance by up to 0.08 A. After running thorough minimization on a poly-A peptide I get: bond amber refmac phenix shelxl Stryer C-N 1.330 1.339 1.331 1.325 1.32 N-CA 1.462 1.482 1.455 1.454 1.47 CA-C 1.542 1.534 1.521 1.546 1.53 CA-CA 3.862 3.874 3.794 3.854 So, which one is "right" ? Cheers, -James

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Phenix download page not working
by Guillaume Gaullier 09 Jul '21

09 Jul '21

Hello, I am trying to download the latest phenix installer, but after I enter all the info on this page ( https://phenix-online.org/phenix_request/index.cgi ) and submit the form, I get the following error message: The server encountered an internal error and was unable to complete your request. Error message: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there was an error in a CGI script. I have not seen this reported in this mailing list yet, but my apologies to the phenix developers if they are already aware of this problem. Maybe related: I could not find anymore the simpler form in which you could check a box saying "I have registered before" so it skips the verification of your academic status and sends you a password right away. I have successfully registered before, with the same email address I am using now, and it would be convenient to still have this fast option. Thank you in advance for any help with this, Guillaume 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

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Postdoc position (Denmark), Structural biology with a focus on metabolite uptake
by Bjørn Panyella Pedersen 07 Jul '21

07 Jul '21

Dear colleagues, Please pass this open postodoc position along to anyone who might be interested. Thanks! Deadline is Aug. 15th. /Bjørn Link: https://www.au.dk/om/stillinger/job/re-advertisement-postdoctoral-position-… ---- Postdoctoral position in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark. The Pedersen group at the Department of Molecular Biology and Genetics, Aarhus University, is looking for a highly skilled and motivated postdoc with an interest in working on metabolite transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. Starting date is negotiable. The project is fully funded by the European Research Council (ERC) for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of metabolite transporting membrane proteins (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The group is part of the Section of Structural Biology at Aarhus University. The candidate A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The Department of Molecular Biology and Genetics The Department of Molecular Biology and Genetics is part of the Faculty of Natural Sciences, Aarhus University and comprises research within the areas of Gene Expression, Molecular Medicine, Structural Biology, Systems Biology and Plant Molecular Biology. There are currently 75 full time scientific staff and 120 PhD students. The department is responsible for two educations: Molecular Biology and Molecular Medicine with a yearly uptake of 160 students in total. Please refer to http://mbg.au.dk/ for further information about The Department of Molecular Biology and Genetics and to https://international.au.dk/ for information on Aarhus University, respectively. The successful candidate is offered: • Access to world-leading research infrastructure. • A research climate inviting lively, open and critical discussion within and across different fields of research. • A working environment with teamwork, close working relations, network activities among young scientists and social activities. • A workplace characterized by professionalism, equality and a healthy work-life balance. The city In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need within a surprisingly small area: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See here for further details on the city and the university.

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Problem with modifying data type
by Stephen Cusack 06 Jul '21

06 Jul '21

Dear Phenix, Whereas in previous version of Phenix (e.g. 1 year ago) I used to be able to run Real-space-refinement for cryoEM models using either a CCP4-map or coefficients from a MTZ file , in recent versions (e.g. currently using 1.19.1-4122-000) when I load an MTZ file, it puts data type File and this stalls upon running, but the data type cannot be changed. Is this a bug or a feature (to stop you using the MTZ file) or am I doing something wrong? thanks Stephen -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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Phenix GUI does not show (on Debian)
by Tim Gruene 05 Jul '21

05 Jul '21

Dear all, I installed phenix 1.19.2.4158 on Debian testing (version 11.0) and Debian stable (version 10.10). On Debian stable, phenix works just fine. On Debian stable (kernel 5.10.0-7-amd64), when I type 'phenix' at the command prompt, I get the usually error about the locale 'en_GB' not being available, and the Phenix splash screen, that disappears automatically. After that, nothing happens. The prompt does not return, phenix is running tg@fibonacci:~$ ps -eLF | grep phenix tg 3823 3776 3823 0 1 33859 83056 6 09:36 pts/1 00:00:00 /xtal/Suites/Phenix/phenix-1.19.2-4158/build/../conda_base/bin/python2.7 -Qnew /xtal/Suites/Phenix/phenix-1.19.2-4158/build/../modules/phenix/wxGUI2/command_line/main.py but no GUI shows up. I can use phenix through ssh on stable, so that this is not an urgent issue. I was just wondering if anyone might have a clue why phenix GUI won't show up on Debian testing? I tried two window managers, KDE and awesomewm on two different computers. Best wishes, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

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