- phenixbb - phenix-online.org

error in Download Request Form for Non-Profit Institutions
by Maxime Cuypers, Ph.D. 26 Jul '21

26 Jul '21

Hello, i get the following error: 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. tried multiple times in firefox. any idea what causes this? cheers, Dr. Maxime Cuypers Researcher, Structural Biology, St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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Problem in real space
by Firdous Tarique 26 Jul '21

26 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 22 Jul '21

22 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 13 Jul '21

13 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 05 Jul '21

05 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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MR-Rosetta crashes during rebuild
by Andrea Piserchio 01 Jul '21

01 Jul '21

Dear all, I am trying to run MR-Rosetta using the gui; [ROSETTA_VERSION]: 2021.16+release.8ee4f02 Phenix version 1.19.2-4158 running on Ubuntu 20.04.2 LTS (20.04, focal) rosetta.run_tests seems to run without errors. As inputs, I use a HHpred file, a reflection file, a sequence (FASTA) file and I tried also providing directly the fragments files from the Robetta server. After generating some starting models, the runs keep crashing during the rebuild stage giving the error messages below. Is there a way to troubleshoot this? It does generate some initial models, so it seems to correctly read the HHPred file and the fasta file. Thank you in advance, Andrea non-zero return code: 139 Failed to run REBUILD from rebuild.log AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Segmentation fault (core dumped) from ROSETTA_CRASH.log: [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT]

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PhD position (Denmark), Structural biology with a focus on metabolite uptake
by Bjørn Panyella Pedersen 01 Jul '21

01 Jul '21

Dear colleagues, Please pass this open PhD position along to anyone who might be interested. Thanks! jobRxiv link: https://bit.ly/3Ak5Far All the best, /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD position is 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 PhD project will be developed in discussion with the selected candidate, 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 project is fully funded by the European Research Council (ERC). 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, but start date is negotiable. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk). Deadline is July 31st 2021. 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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Improvement of low resolution MR phases
by Kajander, Tommi A 29 Jun '21

29 Jun '21

Hello all, I was wondering what would be current best protocols for trying to improve maps/phases for low resolution MR / refinement solutions (5-6 Å resolution). High solvent content of course, dimeric 2:2 protein complex so some NCS averaging and density modification I assume might help (related structures known, currently maps very blobby, clear solution but I think should be able to do better...). Also, refinement suggestions welcome. Best route in phenix? So far worked initially with ccp4. Other suggestions also welcome. Thanks! Tommi Tommi Kajander, Ph.D. Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki, Finland p. +358-50-4480991 http://www.helsinki.fi/kajanderlab

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Macromolecular Crystallography - CSHL Course
by Paul Adams 24 Jun '21

24 Jun '21

Dear Colleagues, The July 16th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 4 through October 19, 2021 is rapidly approaching. Please see the attached announcement, and the official course web site is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=21 please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. We anticipate holding the course in person as long as the pandemic situation continues to improve. Appropriate COVID-19 precautions will be followed to ensure the safety of all participants. Everyone will be required to provide documentary proof of a prior FDA or EMA approved vaccine. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2021 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO), Tom Peat (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be data collection at state-of-the-art beamlines at NSLS-II. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This course is supported with funds provided by the National Institute of General Medical Sciences for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tom, Tassos, Paul, and Jim > Begin forwarded message: > > From: Cold Spring Harbor Laboratory Meetings & Courses <meetmail(a)cshl.edu> > Subject: Macromolecular Crystallography - CSHL Course > Date: June 24, 2021 at 5:20:20 AM PDT > To: pdadams(a)lbl.gov > Reply-To: meetmail(a)cshl.edu > > > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > October 4 - 19, 2021 > Application & Materials Deadline: July 16 > We anticipate that the vaccine situation may sufficiently improve to allow us to offer this course safely in-person. > > All participants will be required to provide documentary proof of a prior FDA or EMA approved vaccine. > Instructors > Janet Newman, CSIRO, Australia (likely remote) > James Pflugrath, Rigaku Americas Corporation (ret.), Texas > Anastassis Perrakis, Netherlands Cancer Institute > Paul Adams, Lawrence Berkeley National Laboratory > Co-Instructor: > Tom Peat, CSIRO, Australia(likely remote) > X-ray crystallography has been the cornerstone of structural biology for half a century, and remains the technique of choice for atomic resolution understanding of macromolecules and for structure guided drug discovery. This intense course combines laboratory and computational instruction to train course participants in the major techniques used to determine three-dimensional structures. It is designed for scientists with a working knowledge of protein structure and function, but who are new to macromolecular crystallography or who wish to increase their in-depth knowledge of macromolecular crystallography. > Topics to be covered include > Basic diffraction theory > Crystallization (proteins, nucleic acids, complexes and membrane proteins) > Synchrotron X-ray sources and optics > Data collection and processing > Structure solution by experimental phasing methods (SAD, MAD, MIR, and others) and molecular replacement > Electron density maps improvement > Model building and refinement > Structure validation > Coordinate deposition > Structure presentation > If you are interested in applying for this course please let us know by submitting the Expression of Interest form via the course website as soon as possible. > Please click this link to go to the Macromolecular Crystallography course website for further info. <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFc…> > > > Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 > -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul <http://cci.lbl.gov/paul> ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Re: [phenixbb] [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
by David Briggs 22 Jun '21

22 Jun '21

Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link). If the second H is added, this breaks the refinement of the Asn-NAG bond. My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box. I hope this fixes your problem. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs ________________________________ From: CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> on behalf of Jiang Xu <foxjuly(a)GMAIL.COM> Sent: Tuesday, June 22, 2021 6:47:36 AM To: CCP4BB(a)JISCMAIL.AC.UK <CCP4BB(a)JISCMAIL.AC.UK> Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine External Sender: Use caution. Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? [image.png] Thank you, Best, Jiang Xu Lin Chen's Research Group University of Southern California ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscm…> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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Macromolecular Crystallography School 2021
by Nicole Larrieux 21 Jun '21

21 Jun '21

Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School 2021 "Structural Biology to enhance high impact research in health and disease” to be held from Sep 20 to Oct 1, 2021 Please find the application form and further information at http://pasteur.uy/novedades/mx2021/ The application deadline is June 30, 2021. For further inquiries contact mx2021(a)pasteur.edu.uy Main Topics: · data collection (remotely @ Diamond synchrotron); · data processing; · phasing and structure determination; · model refinement and validation. 25 participants will be selected, prioritizing advanced PhD students, postdocs and young researchers. No registration fee, please look in the www site for details on application procedures. Participants will have the opportunity to collect data from their own crystals at Diamond Light Source synchrotron via remote access, with the assistance of Diamond staff. The workshop will be virtual considering the pandemics constraints. It will combine excellent lectures with hands-on problem-solving sessions. Tutorials of state-of-the-art software will include XDS, Dials, Phaser, ShelX, Coot, Refmac, Buster-TNT, PISA, among others. Since the workshop is virtual additional participants may elect to attend lectures only. If you wish to do this please complete the registration form and indicate that this is your choice. Invited speakers and tutors: • Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil) • Kevin Cowtan (University of York, UK) • Eleanor Dodson (University of York, UK) • Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK) • Elspeth Garman (University of Oxford, UK) • Richard Garratt (Instituto de Física de São Carlos, Brazil) • Beatriz Guimarāes (Instituto Carlos Chagas Fiocruz, Curitiba, Brazil) • Marin van Heel (Lab. Nacional de Nanotecnologia CNPEM, Campinas, Brazil) • Ronan Keegan (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Eugene Krissinel (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Andrey Lebedev (STFC Rutherford Appleton Lab – CCP4, Didcot, UK) • Natalia Lisa (Instituto de Biología Molecular y Celular, Rosario, Argentina) • Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK) • James Parkhurst (Diamond Light Source, Didcot, UK) • Randy Read (University of Cambridge, UK) • Silvia Russi (Stanford Synchrotron Radiation Lightsource, USA) • Nukri Sanishvili (Argonne National Laboratory, Chicago, USA) • Isabel Usón (Instituto de Biología Molecular de Barcelona, Spain) • Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK) Organizers: Nicole Larrieux, Clinical Biochemist. Institut Pasteur de Montevideo, Uruguay Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); and the Programa Iberoamericano de Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES consortium. Looking forward to seeing you at the Workshop! Nicole, Alejandro, Kyle and Ronan Nicole Larrieux Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/research/labs/molecular-and-structural-microbiology-lab

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Phenix.real_space_refine crash
by Reza Khayat 18 Jun '21

18 Jun '21

Hi, Two files are attached regarding my constant crashing during global minimization. Any help would be appreciated. Refinement is run using the run_Rama_Clash_ss_v1.18.2-3874.eff file. ? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Real space refinement not recognizing modified bases from ribosome
by Firdous Tarique 16 Jun '21

16 Jun '21

Hi I am trying to do real space refinement of a 40S rigid body docked model in a cryoEM map of 4.8 Angstrom resolution. The PDB contains some modified nucleic acid bases due to which the program ends with the following error. Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols; 52 Please edit the model file to resolve the problems and /or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Seems its refinement library is not able to read the modified bases. Can you please advise how to fix this problem. What is the best way to update the library ? Any suggestions are highly appreciated. Best Firdous

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Postdoc position in structural biology at UT Health San Antonio
by Yogesh Gupta 16 Jun '21

16 Jun '21

*Postdoctoral Fellow position at UT Health School of Medicine, San Antonio, Texas* The laboratory of Dr. Yogesh Gupta (http://ccri.uthscsa.edu/YGupta.html) at the University of Texas Health at San Antonio is seeking an enthusiastic Postdoctoral Fellow to study structures and function of RNA modification and chromatin remodeling complexes. We use structural biology (X-ray, NMR, cryo-EM) and cell-based methods to address basic mechanistic questions in viral pathogenesis and pediatric cancers. Gupta laboratory provides a rich multi-disciplinary training environment and access to cutting-edge technologies in structural biology and drug development. Further details of our most recent work can be found here: 1. Nature Communications. 2021 Jun 2; 12: 3287. PMID: 34078893. doi: 10.1038/s41467-021-23594-y <https://www.nature.com/articles/s41467-021-23594-y> 2. Nature Communications. 2020 Jul 24;11(1):3718. PMID: 32709886. doi: 10.1038/s41467-020-17496-8 <https://www.nature.com/articles/s41467-020-17496-8> Preference will be given to applicants with demonstrated experience in protein purification from insect/mammalian cells and structural characterization of protein-nucleic acid complexes by X-ray crystallography or cryo-EM. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work independently but also effectively and collaboratively as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in a related discipline and have no more than 2 years of postdoc experience. The Greehey Children’s Cancer Research Institute (GCCRI) is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. The GCCRI has significant external funding, a large endowment from the state, and links to philanthropic entities. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill County. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry. There is no state income tax in Texas. All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities. Salary is competitive and commensurate with experience. If interested in applying, please send a short description of your research accomplishments and a CV with contact information of 3 references to Dr. Yogesh Gupta (email: guptay(a)uthscsa.edu). Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center San Antonio 8403 Floyd Curl Drive, San Antonio, TX, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Error in Dock in Map
by Firdous Tarique 15 Jun '21

15 Jun '21

Hi I am trying to fit a 40S ribosomal subunit obtained from PDB into a 5 Angstrom EM map using the Dock in Map module. However the program ends with the following error. Model contains both protein and rna/dna atoms.....only one chain type allowed. How can I fix this problem? Any suggestions? Regards Firdous

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C-C sugar linkage in real-space refinement
by Kevin Jude 14 Jun '21

14 Jun '21

I'm trying to refine a cryoEM structure that contains some MAN/C1-TRP/CD1 glycosylations. I've done this successfully in crystallographic reciprocal space refinement, using cif files to define the MAN geometry and the MAN-TRP linkage, plus adding LINK instructions to the pdb file. In this cryoEM structure, though, using the same .cif definition files and similar LINK instruction, the bond is still not defined in the .geo file and instead it's treated as a nonbonded interaction, kicking the mannose away from the indole side chain. The NAG-ASN linkages in the cryoEM structure are fine. Do I need to do anything differently to define these linkages in Real Space Refine compared to phenix.refine? -- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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Turn off side chain optimizations in phenix real space refine?
by Oliver Clarke 11 Jun '21

11 Jun '21

Hi, Is there any way to turn off rotamer fitting/side chain optimization in phenix.real_space_refine? Sometimes it seems to do more harm than good, and repositions sidechains completely out of the density, but I couldn't find how to switch it off. Cheers Oli

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General interest: the history of the European Crystallography Schools
by John R Helliwell 11 Jun '21

11 Jun '21

Dear Colleagues, Th history of the European Crystallography Schools, initiated by Italian colleagues (ECS1 was held in Pavia), is described here at the ECA’s website:- https://ecanews.org/european-crystallography-school/ Several of these previous Schools’ details, but not all as yet, can be found here:- https://ecsx.ecanews.org/ ie replacing the x by the number. The current one ‘Budapest’ being 6. (In each the ECA website is mirrored to the local host organising team.) Greetings, John Emeritus Professor John R Helliwell DSc ECA Past President 2007 to 2010

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European Crystallography School ECS6
by John R Helliwell 10 Jun '21

10 Jun '21

Dear Colleagues, I commend to you the European Crystallography School ECS6. Full details are here:- https://akcongress.com/ecs6/ Best wishes, John Emeritus Professor John R Helliwell DSc

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Restraints for small molecules in macromolecular crystal structures
by Marie Elizabeth Fraser 10 Jun '21

10 Jun '21

Hello, The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement. What do others do? As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX? The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints. Thank you, Marie

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Associate Researcher Position in the KU Protein Structure Laboratory
by Lovell, Scott W 08 Jun '21

08 Jun '21

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is seeking a full-time Associate Researcher to assist with various structural biology projects. As a core laboratory, the PSL collaborates with a diverse range of investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSL manages the structural biology efforts for extramurally funded research projects particularly aimed at inhibitor development. For a full description of the position and to apply, GO TO: https://employment.ku.edu/associate-researcher/19212br Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 __________________________________________________

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Postdoctoral Scholarship Opportunity in the Lane group (PBIO) CFEL/DESY, Hamburg, Germany
by TJ Lane 08 Jun '21

08 Jun '21

Uncovering protein dynamics: developing statistical crystallography Postdoctoral Scholarship Cluster of Excellence: Advanced Imaging of Matter Center for Free Electron Laser Science (CFEL), Hamburg, Germany Protein motion is at the heart of life, but remains challenging to witness firsthand. Proteins move to reading and copying DNA, convert sunlight into chemical energy, and transmit signals between cells, yet our ability to image these functions is limited by the technology we have to image protein dynamics. A new opportunity to meet this challenge is emerging, however, as crystallographic methods advance. We can now collect data from thousands to millions of crystals of the same protein, and it is clear no two crystals are identical. Thus, analyzing their distribution may reveal protein structural fluctuations directly. Can we develop a statistical crystallography to turn these large datasets into knowledge about protein dynamics? Can we use statistical analysis of crystal-to-crystal variation to separate signal from noise in time resolved experiments, revealing protein motion induced by mixing with a ligand or excitation with a pump laser? We seek a computational scientist who will answer these questions. As the ideal candidate, you will have the following key attributes: * A doctoral degree in physics, biophysics, chemistry, applied mathematics or a related field * Working knowledge of macromolecular crystallographic methods and software * A track record of scientific computing and programming * The ability to drive your work independently and show initiative And you will be excited to take on the following responsibilities: * Mathematical modeling of protein dynamics and protein crystal diffraction data * Interpretation and analysis of experimental results * Open-source development to make your insights available to the broader scientific community * Presenting your work in written and oral form to the scientific community * Helping to foster an environment conductive to collaboration, learning, growth, and fun Available immediately is a two-year contract with a competitive salary and the opportunity to work and live in the beautiful and vibrant city of Hamburg, Germany. The group is housed at the Center for Free Electron Laser Science on the vibrant DESY campus (Luruper Chaussee 149, 22761 Hamburg, Germany). This position is funded through the Advanced Imaging of Matter Cluster of Excellence (https://www.cui-advanced.uni-hamburg.de/en.html). The successful candidate will become a fellow of the cluster and have access to career support, training opportunities, and an engaging scientific network via the cluster. The candidate will have additional technical and mentorship support from partners Andrea Thorne, Arwen Pearson, and Nicholas Pearce and their groups during the course of the project. We are an equal opportunity employer. Women and minorities are encouraged to apply and handicapped persons will be preferred given equal qualifications. Application deadline: 17 June 2021 Applications should include a cover letter, a tabular curriculum vitae, and copies of degree certificate(s). Please send applications by email to: < thomas.lane(a)desy.de> For more details, write directly to TJ Lane: <thomas.lane(a)desy.de> Cross-Posting on the AIM Cluster of Excellence page (funding source for this project): https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=4c3ff9d…

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Quick calculation of mean ADP
by Martin Malý 07 Jun '21

07 Jun '21

Dear mailing list members, I would like to calculate the mean ADP of a structure model (PDB) from a Python script using tools in CCTBX/PHENIX. I tried to find out how and dig it from Python source code but I have been unsuccessful yet. Please, how to do it (in Python)? Although It is quite easy to calculate it in on my own directly from PDB for isotropic ADPs, the situation can be a bit complicated for anisotropic ADPs... Thank you. Best regards, Martin Mal ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 03 Jun '21

03 Jun '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JUN 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Twinned data with Phaser
by Thomas, Leonard M. 25 May '21

25 May '21

Hello, I have been working on a structure for a very long while. We have a number of data sets with the good ones mostly around the 3.1-3.2 A range. I do have a determination of the structure but would like to see if I can get the structure determined with a slightly higher resolution data set at around 2.7 A. Problem is the 2.7 data is twinned. Are there settings in Phaser to handle twinned data or is the twinning only handled during refinement? Thank you for any advice, outside of forgetting about the twinned data. Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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Problems with sharpening in Autosharpen
by Carlos HENRIQUE FERNANDES 25 May '21

25 May '21

Dear all, I am facing some problems with sharpening in Autosharpen. My current map is about 3.2 Å resolution, which I obtained after CTF-Refinement and Polishing in Relion. When I use Autosharpen in default parameters, it tells me that are applied an overall Bsharp applied of 220.34 and a final Biso of 87.42; but very little sharpening is done; I was unable to observe a typical helices sharpening at this value of resolution. I did some tests setting progressive Bsharp values (240; 260; 280; 300), but I am still unable to visualize a typical helices sharpening. Has anyone had problems like that? Any tips? Thanks in advance, Carlos.

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Exclude atoms from real space refinement
by Florian Nachon 23 May '21

23 May '21

Hello, I want to exclude a residue from XYZ refinement, but I noticed that my atom selection "not (chain A and resid 100)" is ok for reciprocal-space, but not real-space? Someone encounter a similar problem 10 years ago: http://www.phenix-online.org/pipermail/phenixbb/2012-December/019297.html Is it a known bug? Any clues? Thanx in advance — Florian

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Fwd: [SRCC #47733] Fwd: Phenix GUI showing unreadable squares
by Dong-Hua Chen 19 May '21

19 May '21

Hi All, I asked Stanford cluster admin and he is questioning the CentOS version incompatibilities (see the following). Any suggestions? Thanks Dong-Hua ---------- Forwarded message --------- From: Kilian Cavalotti <srcc-support(a)stanford.edu> Date: Thu, May 13, 2021 at 12:20 PM Subject: Re: [SRCC #47733] Fwd: [phenixbb] Phenix GUI showing unreadable squares To: <donghua.chen(a)gmail.com> Hi Dong-Hua, It looks like the software is built for CentOS 6.10, while Sherlock is running CentOS 7.x, so incompatibilities are likely. Is there a way to rebuild it from source. maybe? Cheers, -- *Kilian Cavalotti* Stanford Research Computing Center *Sherlock // *web <https://www.sherlock.stanford.edu> | docs <https://www.sherlock.stanford.edu/docs> | status <https://status.sherlock.stanford.edu> | news <https://news.sherlock.stanford.edu>47733:1231609

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Cryo-EM Facility Manager - Berkeley California
by Paul Adams 18 May '21

18 May '21

Dear Colleagues, I would like to draw your attention to a job opening here in Berkeley California, for a Cryo-EM Facility Manager: https://lbl.referrals.selectminds.com/jobs/cryo-em-facility-manager-3801 This position requires expertise in biological cryo electron microscopy (cryo-EM). The successful candidate will be responsible for maintaining the in-house transmission electron microscopes (TEMs) and accessory equipment in excellent working order as well as training new users, scheduling access, and assisting with the collection of high-quality data. Duties will include providing complex technical support for sophisticated biotech-laboratory equipment including maintenance, calibration, repair and troubleshooting of instrumentation, control systems, experimental apparatuses, computers, and peripheral equipment as well as coordinating and scheduling vendor related maintenance and repairs. This is a full time, 3 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion. Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/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, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Deadline today -- IUCr SARS-CoV-2 special symposia.
by Pearce, N.M. (Nick) 17 May '21

17 May '21

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural biology of coronaviruses This session covers new structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. - New methods to fight the pandemic This session covers new methods in crystallography and structural biology to better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in computational methods, beamline instrumentation and integrative structural biology. - Crystallography against Corona This session covers the efforts of the crystallographic community to find drug candidates for COVID-19 both in-silico and in the lab by using structural models of viral proteins. - Using crystallography for education during the pandemic Using crystallography for education during the pandemic *** Please submit your abstracts today! If this isn’t possible, email us to let us know you intend to submit an abstract in the coming days! *** For each session, 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Session co-chairs

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questions about using experimental phases in phenix.refine
by David A Case 15 May '21

15 May '21

I'm trying to use experimental phases derived from an cryoEM density map do carry out reciprocal space refinement in phenix.refine. I used phenix.map_box to get the map coefficients, and then the CCP4 program chltofom (with the -colin-phifom flag) to create the HL coefficients from F/PHI computed from the electron density map. 1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set: | normalized target function (mlhl) (work): -5862.311069 | | target function (mlhl) not normalized (work): -6438670043.811632 and attempted refinements more or less destroy my protein and increases both the mlhl target value and the R-factors. Is there an example data set I could access to help me find out what I'm doing wrong? (Using the ml target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to work well, and has a postive target function, but seems sub-optimal if phase information is available.) 2. Is there a way to do a "simple" least-squares refinement, minimizing sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as vectors? Does the ls target perhaps do this if use_experimental_phases=True? Usual apologies if there is some great tutorial on this that I've not found. ...thanks...dave case

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Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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Scientific software programmer at UCLA
by Johan Hattne 12 May '21

12 May '21

Dear all; The Gonen lab at UCLA's Department of Biological Chemistry is looking for a research specialist in scientific software programming to develop software for computational biological image analysis. The Gonen lab works toward understanding how membrane proteins help cells maintain homeostasis. To that end, the lab studies channels, transporters, and receptors, structurally and functionally. More information about the lab can be found by visiting https://cryoem.ucla.edu/. Details about the position and application instructions here: https://hhmi.wd1.myworkdayjobs.com/External/job/University-of-California-Lo… // Best wishes; Johan

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Help with den refine
by Alex Singer 11 May '21

11 May '21

Hi: I recently installed the Linux-64 version of phenix1.19.2-4158 and used the command line to run phenix.den_refine. The command was just Phenix.den_refine xxx_refine_25.pdb xxx_refine_25.mtz (xxx is just the name of the project, and is made up, but I did the same thing for two different projects) And then it ran for a while until it started the initial minimization before the den routine, ie coordinate minimization before annealing and then it crashed with the error message TypeError: %d format; a number is required, not Autotype I believe this is a python error, but is there something straight-forward that I can do about this so that den_refine can work? Thanks for your help Dr. Alex U. Singer

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Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Andrea Thorn 11 May '21

11 May '21

Dear all, Gianluca Santoni and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea -- Dr. Andrea Thorn | group leader andrea.thorn(a)uni-hamburg.de HARBOR (Institute for Nanostructure and Solid State Physics), Universität Hamburg Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany Tel. +49 (0)40 42838 3651 www.thorn-lab.de | www.insidecorona.de

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Re: [phenixbb] real space rotamer restrains
by Pavel Afonine 10 May '21

10 May '21

Dear Leonid, thanks for sharing this and for your patience while waiting for the fix! All the best! Pavel On 5/10/21 06:36, Leonid Sazanov wrote: > Dear Pavel, > > Many thanks for this fix! > > Using local_grid_search now does not produce those rare outliers - > illustrated in the attachment for the benefit of others. > > "Before" is the earlier version refine run and "after" is using > phenix/1.20-dev-4224. > > Best wishes, > > Leonid > > > On 27.04.21 01:46, Pavel Afonine wrote: >> Dear Leonid, >> >> this is fixed now, residues won't leave good density any more. Next >> nightly build (dev-4218): >> >> http://phenix-online.org/download/nightly_builds.cgi?show_all=1 >> >> should have the fix. >> >> Please note, this is not the official released version meaning that >> while it is automatically tested it is not tested as thoroughly as >> regular official releases. With this in mind, it is advisable to keep >> around whatever version you are using currently just in case while >> using the latest nightly! >> >> Let us know should you discover any more problems! >> >> Cheers, >> Pavel >> >> >> On 4/26/21 13:53, Pavel Afonine wrote: >>> Dear Leonid, >>> >>> thanks for sharing files and my apologies for slow replies. >>> >>> I was able to reproduce the issue and I'm on it investigating right >>> now. I agree, this looks bad! >>> >>> More soon as progress happens. >>> >>> All the best! >>> Pavel >>> >>>

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Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Gianluca SANTONI 10 May '21

10 May '21

Dear all, Andrea Thorn and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea

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Re: [phenixbb] quick demo of phenix.autosol ?
by James Holton 06 May '21

06 May '21

Thank you all for the excellent suggestions! I think the built-in tutorials are a good place to start. I noticed a couple of things: 1) the autosol GUI "Status" tab always shows the number of sites to be zero, despite having solved the structure. Is that a bug? 2) the autosol GUI requires data filenames to be non-unique after removing the directory names. These days a rather large fraction of data files are called "XDS_ASCII.HKL". Now, for me personally, I don't mind opening a shell and making some links, but the students are sometimes confounded by that. Am I not doing the workflow right here? Again, thank you all for all the effort that goes into making Phenix great! -James Holton MAD Scientist

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Phenix GUI showing unreadable squares
by Dong-Hua Chen 06 May '21

06 May '21

Hi All, I am trying to install Phenix version 1.19.2-4158 on a node of a cluster and the installation was complete. After I tried to run phenix, the pop-up window showed lots of unrecognized small squares instead of letters (see the picture attached). I also tried to install the version 1.18.2 and got the same problem. Any suggestions would be greatly appreciated. Thanks, Dong-Hua

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Postdoc position micro electron diffraction / single particle analysis @Braunschweig/Germany
by Blankenfeldt, Wulf 04 May '21

04 May '21

Dear colleagues, together with Rolf Müller (one of this year's Leibniz Prize winners in Germany) we are currently looking for a postdoc to help us establish micro electron diffraction (and single particle analysis) in natural product research. Details about the position can be found here: https://www.helmholtz-hzi.de/en/career/open-positions/jobs/view/job/details… I'd be grateful if you could inform potential candidates. Regards, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] Model required for combine_focused_maps
by Tom Terwilliger 03 May '21

03 May '21

Hi Fengwei, The model has to be pretty good as it is used to evaluate the maps. I would improve the model first, at least by refinement , then combine the maps, then maybe iterate the whole process with a new model. -Tom T On Mon, May 3, 2021 at 14:19 Zheng, Fengwei <Fengwei.Zheng(a)vai.org> wrote: > Dear Phenix developers: > > Thank you for developing this so powerful and elegant software packages > for our community! > > I am a newbie in cryoEM, and recently I got a consensus map, and split it > into two parts to do the further focused refinement, after that I want to > combine them together, and then to build my model, I learned that this > "combine focused maps" module in Phenix can achieve this, I read through > this online tutorial ( > https://www.phenix-online.org/documentation/reference/combine_focused_maps.…), > for the starting input files, I seem need to provide my initial/consensus > map, two focused maps and a model, but I have a question about this > provided model: > > 1st, need me to provide my final refined model (i.e. I need to finish my > model building firstly according to my two focused maps), or I can use a > homologue model for this combination? > > 2nd, if I use a homologue model that only can be roughly fitted into my > consensus map, will this affect my final combination results? > > Appreciate! > > Best, > Fengwei > > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Error at fix_insertions_deletions
by Carlos HENRIQUE FERNANDES 03 May '21

03 May '21

Hello all! I'am facing a problem running the phenix.fix_insertions_deletions. I'am using in the command line: phenix.fix_insertions_deletions sharpened_map.ccp4 resolution=3.5 protein.pdb seq.dat I've been encountering this error: File "/usr/local/phenix-1.19.2-4158/build/../modules/phenix/phenix/command_line/fix_insertions_deletions.py", line 7, in <module> run_program(program_class=fix_insertions_deletions.Program) File "/usr/local/phenix-1.19.2-4158/modules/cctbx_project/iotbx/cli_parser.py", line 72, in run_program task.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/programs/fix_insertions_deletions.py", line 515, in run self.fix_insertions_deletions.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1331, in run self.run_macro_cycles() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1464, in run_macro_cycles self.run_cycles(mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1485, in run_cycles self.overall_rebuild_worst_residues(icycle,mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1528, in overall_rebuild_worst_residues mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1027, in rebuild_worst_residues map_coeffs=map_coeffs) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 589, in rebuild_one_loop end_rebuild=end_rebuild,) UnboundLocalError: local variable 'new_model' referenced before assignment Has anyone encountered this error before? Thanks in advance, Carlos Fernandes

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quick demo of phenix.autosol ?
by James Holton 02 May '21

02 May '21

Hello all, I'm involved in an X-ray course at Stanford this coming week and one of the things we want to do is demonstrate things like phenix.autosol. However, typical run times with borderline data and default settings can be more than a few minutes. Can anyone recommend a test data set / settings where phenix.autosol finishes very quickly? I was going to try and whip something up that is small, moderate resolution, screaming phasing signal, etc. However, since I'm sure many on this mailing list have done this hundreds of times you no doubt have a favorite example off the top of your head? thanks again! -James Holton MAD Scientist

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Refinement of a b-Strand swapped into the sheet of the symmetry related copy
by Matthias Uthoff 28 Apr '21

28 Apr '21

Hi phenixbb, I am working on a homodimer. Each protein has an internal b-sheet with three b-strands, however the sheets swap their middle strands. So a sheet consists of one strand from molecule A surrounded by two strands from molecule B or vice versa. As I am at 3 A resolution, I would like to set secondary structure restraints including correct hydrogen bonding between the strands of the two molecules. My problem: There is only one protein in the ASU and the "other" molecule is in deed just a symmetry mate. Phenix is not able to automatically detect this and if I provide the restraints myself, phenix discards them as it is falsely assuming the b-sheet is intramolecularly (all on chain A) and hence the strands are 30ish A apart. What is the best way of refining this feature? Thanks in advance, Matthias -- Matthias Uthoff, PhD Student University of Cologne Institute for Biochemistry Zülpicher Straße 47 D-50674 Cologne Phone: +49 221 470 3211 E-Mail:[email protected] Internet:http://px.uni-koeln.de

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