- phenixbb - phenix-online.org

Phenix GUI showing unreadable squares
by Dong-Hua Chen 05 May '21

05 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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Online Course on Neutron Scattering Applications in Structural Biology (HANDS2021)
by Meilleur, Flora 27 Apr '21

27 Apr '21

ORNL Online Course on Neutron Scattering Applications in Structural Biology: https://conference.sns.gov/event/291/ Lectures: June 21 - June 25, 2021 Tutorials: June 28 - 30, 2021 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 14, 2021: https://conference.sns.gov/event/291/registrations/ This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Lectures will cover basic concepts, sample preparation, instrumentation and applications. Data collection and processing will be discussed in tutorials.

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temp files
by James Holton 26 Apr '21

26 Apr '21

Hello all, Is there a way to configure phenix at install time (or perhaps post-install) to put temporary files under /tmp ? I just had to delete 20e6 temp files over NFS from a single user's phenix ligand identification run. The delete took almost a month. Apologies if I am neglecting to look somewhere obvious in the documentation, Happy Weekend! -James Holton MAD Scientist

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Job posting: Scientist-I (Structural biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 21 Apr '21

21 Apr '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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Caltech Postdoc Position
by Hoelz, Andre 19 Apr '21

19 Apr '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit two outstanding postdoctoral scientists in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, and/or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills, who is able to carry out a structure determination project from the development of recombinant protein expression systems to structure refinement. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The positions are available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu<mailto:[email protected]>). Selected Publications Lin, D. H., Hoelz, A.* (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A.,* (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D.,# Stuwe, T.,# Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A.* (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T.,# Bley, C.J.,# Thierbach, K.,# Petrovic, S.,# Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T.,# Correia, A.,# Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A.,* Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643. --- André Hoelz, Ph.D. Faculty Scholar, Howard Hughes Medical Institute Investigator, Heritage Medical Research Institute Professor of Chemistry and Biochemistry Division of Chemistry and Chemical Engineering California Institute of Technology <x-apple-data-detectors://2><x-apple-data-detectors://2>1200 East California Boulevard<x-apple-data-detectors://2> Pasadena, CA 91125<x-apple-data-detectors://2> <x-apple-data-detectors://2><x-apple-data-detectors://2>U.S.A.<x-apple-data-detectors://2> Tel: 1-626-395-8480<tel:1-626-395-8480> (office) Tel: 1-626-395-3152<tel:1-626-395-3152> (lab) http://ahweb.caltech.edu<http://ahweb.caltech.edu/>

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